[SCM] read SAM/BAM nucleotide sequence aligment database files branch, meta, updated. meta/1.31-1+b1-3-g4f4dfcc
Charles Plessy
plessy at debian.org
Sun Jan 29 06:07:47 UTC 2012
The following commit has been merged in the meta branch:
commit 4f4dfcc47c3892737ffc7a3abd16b8ea4a97cb1a
Author: Charles Plessy <plessy at debian.org>
Date: Sun Jan 29 15:05:22 2012 +0900
Build logs for libbio-samtools-perl_1.33-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index 757ade6..a20dbcf 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,52 +2,65 @@
Hash: SHA256
Format: 1.8
-Date: Wed, 23 Nov 2011 16:26:32 +0900
+Date: Sun, 29 Jan 2012 14:38:27 +0900
Source: libbio-samtools-perl
Binary: libbio-samtools-perl
Architecture: source amd64
-Version: 1.32-1
+Version: 1.33-1
Distribution: unstable
Urgency: low
Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
- libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files
+ libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing
Changes:
- libbio-samtools-perl (1.32-1) unstable; urgency=low
+ libbio-samtools-perl (1.33-1) unstable; urgency=low
.
- [36ac64b] New upstream release.
- [dfb9312] Depend on BioPerl 1.6.901, following Upstream.
+ * [5fd8406] New upstream release 1.33
+ .
+ [ Nathan Handler ]
+ * [4058f51] Add myself to Uploaders and debian/copyright
+ * [01985a1] Remove version from perl Build-Depend. oldstable has 5.10
+ * [5b63fda] Don't Build-Depend on libmodule-build-perl (included in
+ core since 5.10)
+ * [af3530d] Remove version from libbio-perl-perl Build-Depend. Nothing
+ older in archive
+ * [d6d6dca] Don't Depend on perl, ${perl:Depends} will pull it in
+ * [64ad8db] Turn short description into noun phrase based on abstract
+ in upstream META.json
+ .
+ [ Charles Plessy ]
+ * [bb4b659] Renamed debian/upstream-metadata.yaml to debian/upstream.
Checksums-Sha1:
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- ac6d745665cb500a0d42e48ddc1811fdd1a84901 7084 libbio-samtools-perl_1.32-1.debian.tar.gz
- d4bb121221195004e586b9de7398d99d5fe9b4dd 208154 libbio-samtools-perl_1.32-1_amd64.deb
+ 0d2c453541cf0263c372a81da2cb30a5e8f420d1 2148 libbio-samtools-perl_1.33-1.dsc
+ 109d5bfdb5c7629d5a82971915b25f9912c77ae8 332340 libbio-samtools-perl_1.33.orig.tar.gz
+ 1999efb61550cdc26001216d6817f3816e0df70b 7345 libbio-samtools-perl_1.33-1.debian.tar.gz
+ c2af5da434a3f4d38b952636721e10ebb33e17c8 208410 libbio-samtools-perl_1.33-1_amd64.deb
Checksums-Sha256:
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- 44296d2eeb0e2db400ad50d6bda99287d567e3031e6681d35666f0df85d6e712 208154 libbio-samtools-perl_1.32-1_amd64.deb
+ 608b875f022476a8fabf7779f88b7e93839371490d5b65caf3c7caaf29fb2eb4 2148 libbio-samtools-perl_1.33-1.dsc
+ b908b829b76097b4ee8015fe0271a2bd56a1bbaa2ca6698a96c741d80d2dfc70 332340 libbio-samtools-perl_1.33.orig.tar.gz
+ b278ea7525f20c7c0f156901d9dfde16c9313edb7f770a8334984a6e7f0cbd70 7345 libbio-samtools-perl_1.33-1.debian.tar.gz
+ 4d08ba181d2d3eeabc80d3c129eb6dc6757251288b2b3ea52cf0bb4762def094 208410 libbio-samtools-perl_1.33-1_amd64.deb
Files:
- 20ed15a174e1a7e4f3390e2bfae2d438 2168 perl optional libbio-samtools-perl_1.32-1.dsc
- 566f8eb1a84856da3e524b32f3edfd47 332281 perl optional libbio-samtools-perl_1.32.orig.tar.gz
- 4570cb3b9a7b65d1bdf83b2cf11d2870 7084 perl optional libbio-samtools-perl_1.32-1.debian.tar.gz
- 1078d51844a57e10b03442e1b08b6c74 208154 perl optional libbio-samtools-perl_1.32-1_amd64.deb
+ 3ff912e60c479ab04b2d27234d2b104a 2148 perl optional libbio-samtools-perl_1.33-1.dsc
+ 68a9c89034663597dd89391012980955 332340 perl optional libbio-samtools-perl_1.33.orig.tar.gz
+ 8e370c47251140daa558c25125f6ffee 7345 perl optional libbio-samtools-perl_1.33-1.debian.tar.gz
+ d64f08bf376fd544649ee54dc5de69fc 208410 perl optional libbio-samtools-perl_1.33-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index ee1076d..4692d94 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,26 +1,29 @@
-sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
+sbuild (Debian sbuild) 0.62.6 (07 Dec 2011) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ libbio-samtools-perl 1.32-1 (amd64) 23 Nov 2011 16:32 ║
+║ libbio-samtools-perl 1.33-1 (amd64) 29 janv. 2012 14:58 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: libbio-samtools-perl
-Version: 1.32-1
-Source Version: 1.32-1
+Version: 1.33-1
+Source Version: 1.33-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/libbio-samtools-perl-7hujaQ/libbio-samtools-perl-1.32' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/libbio-samtools-perl-7hujaQ' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-bd70c3c0-bc26-4798-ae04-226ba7ea3e00' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/libbio-samtools-perl-6kQ4P9/libbio-samtools-perl-1.33' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/libbio-samtools-perl-6kQ4P9' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-df4e8c68-0b8c-4cee-8c45-91c5cda80ab0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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
+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-en
+Hit ftp://ftp.jaist.ac.jp sid/main Translation-fr
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -35,14 +38,14 @@ Reading state information...
Local sources
─────────────
-libbio-samtools-perl_1.32-1.dsc exists in .; copying to chroot
+libbio-samtools-perl_1.33-1.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-M1FXb5/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-R4q2PM/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -54,11 +57,19 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-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), debhelper (>= 8), libmodule-build-perl, perl-modules, perl (>= 5.8), zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl (>= 1.6.901)
-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), debhelper (>= 8), libmodule-build-perl, perl-modules, perl (>= 5.8), zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl (>= 1.6.901)
-dpkg-deb: building package `sbuild-build-depends-libbio-samtools-perl-dummy' in `/«BUILDDIR»/resolver-1_87rb/apt_archive/sbuild-build-depends-libbio-samtools-perl-dummy.deb'.
+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/714 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 ... 10824 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), debhelper (>= 8), perl, zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl
+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), debhelper (>= 8), perl, zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl
+dpkg-deb: building package `sbuild-build-depends-libbio-samtools-perl-dummy' in `/«BUILDDIR»/resolver-Sl_r7j/apt_archive/sbuild-build-depends-libbio-samtools-perl-dummy.deb'.
OK
Reading package lists...
@@ -71,13 +82,14 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- debhelper file gettext gettext-base groff-base html2text intltool-debian
- libbam-dev libbio-perl-perl libcroco3 libdata-stag-perl libffi5 libglib2.0-0
- libio-string-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libbam-dev libbio-perl-perl libcroco3 libdata-stag-perl
+ libffi5 libglib2.0-0 libio-string-perl libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
- dh-make gettext-doc groff bioperl libmath-random-perl
- libxml-sax-expatxs-perl less www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc groff bioperl
+ libmath-random-perl libxml-sax-expatxs-perl less www-browser
+ libmail-box-perl
Recommended packages:
curl wget lynx-cur autopoint bioperl-run libbio-perl-run-perl libace-perl
libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl
@@ -92,29 +104,38 @@ Recommended packages:
libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libglib2.0-data
shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- debhelper file gettext gettext-base groff-base html2text intltool-debian
- libbam-dev libbio-perl-perl libcroco3 libdata-stag-perl libffi5 libglib2.0-0
- libio-string-perl libmagic1 libpcre3 libpipeline1 libunistring0 libxml2
- man-db po-debconf sbuild-build-depends-libbio-samtools-perl-dummy zlib1g-dev
+ bsdmainutils debhelper file gettext gettext-base groff-base html2text
+ intltool-debian libbam-dev libbio-perl-perl libcroco3 libdata-stag-perl
+ libffi5 libglib2.0-0 libio-string-perl libmagic1 libpcre3 libpipeline1
+ libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-libbio-samtools-perl-dummy zlib1g-dev
+0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded.
+Need to get 9794 kB/16.6 MB of archives.
+After this operation, 43.9 MB of additional disk space will be used.
+Get:1 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libglib2.0-0 amd64 2.30.2-6 [1846 kB]
+Get:2 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libxml2 amd64 2.7.8.dfsg-7 [895 kB]
+Get:3 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main bsdmainutils amd64 9.0.1 [210 kB]
+Get:4 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main debhelper all 9.20120115 [693 kB]
+Get:5 ftp://ftp.jaist.ac.jp/pub/Linux/Debian/ sid/main libbio-perl-perl all 1.6.901-2 [6151 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/16.2 MB of archives.
-After this operation, 46.4 MB of additional disk space will be used.
+Fetched 9794 kB in 29s (331 kB/s)
Selecting previously unselected package libpipeline1.
-(Reading database ... 10825 files and directories currently installed.)
+(Reading database ... 10824 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-5_amd64.deb) ...
Selecting previously unselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-4_amd64.deb) ...
Selecting previously unselected package libffi5.
Unpacking libffi5 (from .../libffi5_3.0.10-3_amd64.deb) ...
Selecting previously unselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-4_amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.30.2-6_amd64.deb) ...
Selecting previously unselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-5_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-7_amd64.deb) ...
Selecting previously unselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-2_amd64.deb) ...
Selecting previously unselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-5_amd64.deb) ...
+Selecting previously unselected package bsdmainutils.
+Unpacking bsdmainutils (from .../bsdmainutils_9.0.1_amd64.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
Selecting previously unselected package man-db.
@@ -132,9 +153,9 @@ Unpacking gettext (from .../gettext_0.18.1.1-5_amd64.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.9.11_all.deb) ...
+Unpacking debhelper (from .../debhelper_9.20120115_all.deb) ...
Selecting previously unselected package libbam-dev.
Unpacking libbam-dev (from .../libbam-dev_0.1.18-1_amd64.deb) ...
Selecting previously unselected package libio-string-perl.
@@ -142,7 +163,7 @@ Unpacking libio-string-perl (from .../libio-string-perl_1.08-2_all.deb) ...
Selecting previously unselected package libdata-stag-perl.
Unpacking libdata-stag-perl (from .../libdata-stag-perl_0.11-2_all.deb) ...
Selecting previously unselected package libbio-perl-perl.
-Unpacking libbio-perl-perl (from .../libbio-perl-perl_1.6.901-1_all.deb) ...
+Unpacking libbio-perl-perl (from .../libbio-perl-perl_1.6.901-2_all.deb) ...
Selecting previously unselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously unselected package sbuild-build-depends-libbio-samtools-perl-dummy.
@@ -150,11 +171,14 @@ Unpacking sbuild-build-depends-libbio-samtools-perl-dummy (from .../sbuild-build
Setting up libpipeline1 (1.2.0-5) ...
Setting up libpcre3 (8.12-4) ...
Setting up libffi5 (3.0.10-3) ...
-Setting up libglib2.0-0 (2.30.2-4) ...
+Setting up libglib2.0-0 (2.30.2-6) ...
No schema files found: doing nothing.
-Setting up libxml2 (2.7.8.dfsg-5) ...
+Setting up libxml2 (2.7.8.dfsg-7) ...
Setting up libcroco3 (0.6.2-2) ...
Setting up libunistring0 (0.9.3-5) ...
+Setting up bsdmainutils (9.0.1) ...
+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 (2.6.0.2-3) ...
Building database of manual pages ...
@@ -164,12 +188,12 @@ Setting up gettext-base (0.18.1.1-5) ...
Setting up html2text (1.3.2a-15) ...
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 (8.9.11) ...
+Setting up po-debconf (1.0.16+nmu2) ...
+Setting up debhelper (9.20120115) ...
Setting up libbam-dev (0.1.18-1) ...
Setting up libio-string-perl (1.08-2) ...
Setting up libdata-stag-perl (0.11-2) ...
-Setting up libbio-perl-perl (1.6.901-1) ...
+Setting up libbio-perl-perl (1.6.901-2) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-libbio-samtools-perl-dummy (0.invalid.0) ...
@@ -177,9 +201,9 @@ Setting up sbuild-build-depends-libbio-samtools-perl-dummy (0.invalid.0) ...
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 2.6.39-bpo.2-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.22-1 dpkg-dev_1.16.1.1 g++-4.6_4.6.2-5 gcc-4.6_4.6.2-5 libc6-dev_2.13-21 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 linux-libc-dev_3.1.1-1
-Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.22-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 coreutils_8.13-3 cpp_4:4.6.1-3 cpp-4.6_4.6.2-5 dash_0.5.7-2 debconf_1.5.41 debfoster_2.7-1.1 debhelper_8.9.11 debian-archive-keyring_2010.08.28 debianutils_4.0.4 diffutils_1:3.2-1 dpkg_1.16.1.1 dpkg-dev_1.16.1.1 e2fslibs_1.42~WIP-2011-11-20-1 e2fsprogs_1.42~WIP-2011-11-20-1 fakeroot_1.18.1-1 file_5.09-2 findutils_4.4.2-1+b1 g++_4:4.6.1-3 g++-4.6_4.6.2-5 gcc_4:4.6.1-3 gcc-4.6_4.6.2-5 gcc-4.6-base_4.6.2-5 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-2 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.13 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-4 libattr1_1:2.4.46-3 libbam-dev_0.1.18-1 libbio-perl-perl_1.6.901-1 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-21 libc-dev-bin_2.13-21 libc6_2.13-21 libc6-dev_2.13-21 libclass-isa-perl_0.36-2 libcomerr2_1.42~WIP-2011-11-20-1 libcroco3_0.6.2-2 libdata-stag-perl_0.11-2 libdb5.1_5.1.25-11 libdpkg-perl_1.16.1.1 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-5 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-4 libgmp10_2:5.0.2+dfsg-2 libgomp1_4.6.2-5 libgpm2_1.20.4-4 libio-string-perl_1.08-2 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_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-6 libpam-modules-bin_1.1.3-6 libpam-runtime_1.1.3-6 libpam0g_1.1.3-6 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-5 libreadline6_6.2-8 libselinux1_2.1.0-4 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-11-20-1 libstdc++6_4.6.2-5 libstdc++6-4.6-dev_4.6.2-5 libswitch-perl_2.16-2 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-5 linux-libc-dev_3.1.1-1 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.19.1-5 multiarch-support_2.13-21 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.14.2-5 perl-base_5.14.2-5 perl-modules_5.14.2-5 po-debconf_1.0.16+nmu1 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbio-samtools-perl-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.13 sysvinit_2.88dsf-13.13 sysvinit-utils_2.88dsf-13.13 tar_1.26-3 tzdata_2011n-1 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Kernel: Linux 3.1.0-1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.22-5 dpkg-dev_1.16.1.2 g++-4.6_4.6.2-12 gcc-4.6_4.6.2-12 libc6-dev_2.13-24 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 linux-libc-dev_3.2.1-2
+Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.24 bash_4.2-1 binutils_2.22-5 bsdmainutils_9.0.1 bsdutils_1:2.20.1-1.2 build-essential_11.5 bzip2_1.0.6-1 coreutils_8.13-3 cpp_4:4.6.2-4 cpp-4.6_4.6.2-12 dash_0.5.7-2 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_9.20120115 debian-archive-keyring_2010.08.28 debianutils_4.2 diffutils_1:3.2-1 dpkg_1.16.1.2 dpkg-dev_1.16.1.2 e2fslibs_1.42-1 e2fsprogs_1.42-1 fakeroot_1.18.2-1 file_5.09-2 findutils_4.4.2-4 g++_4:4.6.2-4 g++-4.6_4.6.2-12 gcc_4:4.6.2-4 gcc-4.6_4.6.2-12 gcc-4.6-base_4.6.2-12 gettext_0.18.1.1-5 gettext-base_0.18.1.1-5 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.10-1 groff-base_1.21-6 gzip_1.4-2 hostname_3.10 html2text_1.3.2a-15 initscripts_2.88dsf-21 insserv_1.14.0-2.2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-5 libattr1_1:2.4.46-5 libbam-dev_0.1.18-1 libbio-perl-perl_1.6.901-2 libblkid1_2.20.1-1.2 libbz2-1.0_1.0.6-1 libc-bin_2.13-24 libc-dev-bin_2.13-24 libc6_2.13-24 libc6-dev_2.13-24 libclass-isa-perl_0.36-3 libcomerr2_1.42-1 libcroco3_0.6.2-2 libdata-stag-perl_0.11-2 libdb4.7_4.7.25-20 libdb4.8_4.8.30-11 libdb5.1_5.1.29-1 libdpkg-perl_1.16.1.2 libffi5_3.0.10-3 libgc1c2_1:7.1-8 libgcc1_1:4.6.2-12 libgdbm3_1.8.3-10 libglib2.0-0_2.30.2-6 libgmp10_2:5.0.3+dfsg-1 libgmp3c2_2:4.3.2+dfsg-2 libgomp1_4.6.2-12 libio-string-perl_1.08-2 liblocale-gettext-perl_1.05-7+b1 liblzma2_5.1.1alpha+20110809-2 liblzma5_5.1.1alpha+20110809-3 libmagic1_5.09-2 libmount1_2.20.1-1.2 libmpc2_0.9-4 libmpfr4_3.1.0-3 libncurses5_5.9-4 libpam-modules_1.1.3-7 libpam-modules-bin_1.1.3-7 libpam-runtime_1.1.3-7 libpam0g_1.1.3-7 libpcre3_8.12-4 libpipeline1_1.2.0-5 libpod-plainer-perl_1.03-1 libquadmath0_4.6.2-12 libreadline6_6.2-8 libselinux1_2.1.0-4.1 libsepol1_2.1.0-1.2 libslang2_2.2.4-5 libss2_1.42-1 libstdc++6_4.6.2-12 libstdc++6-4.6-dev_4.6.2-12 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7+b1 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-4 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20 libuuid1_2.20.1-1.2 libxml2_2.7.8.dfsg-7 linux-libc-dev_3.2.1-2 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28.1 make_3.81-8.1 man-db_2.6.0.2-3 mawk_1.3.3-16 mount_2.20.1-1.2 multiarch-support_2.13-24 ncurses-base_5.9-4 ncurses-bin_5.9-4 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-3 perl_5.14.2-6 perl-base_5.14.2-6 perl-modules_5.14.2-6 po-debconf_1.0.16+nmu2 readline-common_6.2-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libbio-samtools-perl-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-21 sysvinit_2.88dsf-21 sysvinit-utils_2.88dsf-21 tar_1.26-4 tzdata_2011n-2 ucf_3.0025+nmu2 util-linux_2.20.1-1.2 xz-utils_5.1.1alpha+20110809-3 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -189,10 +213,10 @@ Package versions: apt_0.8.15.9 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (libbio-samtools-perl_1.32-1.dsc)
-dpkg-source: info: extracting libbio-samtools-perl in libbio-samtools-perl-1.32
-dpkg-source: info: unpacking libbio-samtools-perl_1.32.orig.tar.gz
-dpkg-source: info: unpacking libbio-samtools-perl_1.32-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (libbio-samtools-perl_1.33-1.dsc)
+dpkg-source: info: extracting libbio-samtools-perl in libbio-samtools-perl-1.33
+dpkg-source: info: unpacking libbio-samtools-perl_1.33.orig.tar.gz
+dpkg-source: info: unpacking libbio-samtools-perl_1.33-1.debian.tar.gz
Check disc space
────────────────
@@ -209,8 +233,8 @@ SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-bd70c3c0-bc26-4798-ae04-226ba7ea3e00
-SCHROOT_UID=31051
+SCHROOT_SESSION_ID=sid-amd64-sbuild-df4e8c68-0b8c-4cee-8c45-91c5cda80ab0
+SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
TERM=xterm
@@ -221,20 +245,20 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package libbio-samtools-perl
-dpkg-buildpackage: source version 1.32-1
+dpkg-buildpackage: source version 1.33-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build libbio-samtools-perl-1.32
+ dpkg-source --before-build libbio-samtools-perl-1.33
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
dh_clean
- dpkg-source -b libbio-samtools-perl-1.32
+ dpkg-source -b libbio-samtools-perl-1.33
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building libbio-samtools-perl using existing ./libbio-samtools-perl_1.32.orig.tar.gz
-dpkg-source: info: building libbio-samtools-perl in libbio-samtools-perl_1.32-1.debian.tar.gz
-dpkg-source: info: building libbio-samtools-perl in libbio-samtools-perl_1.32-1.dsc
+dpkg-source: info: building libbio-samtools-perl using existing ./libbio-samtools-perl_1.33.orig.tar.gz
+dpkg-source: info: building libbio-samtools-perl in libbio-samtools-perl_1.33-1.debian.tar.gz
+dpkg-source: info: building libbio-samtools-perl in libbio-samtools-perl_1.33-1.dsc
debian/rules build
dh build
dh_testdir
@@ -243,11 +267,11 @@ make[1]: Entering directory `/«PKGBUILDDIR»'
SAMTOOLS=/usr/include/samtools dh_auto_configure
Found /usr/include/samtools/bam.h and /usr/lib/libbam.a.
Created MYMETA.yml and MYMETA.json
-Creating new 'Build' script for 'Bio-SamTools' version '1.32'
+Creating new 'Build' script for 'Bio-SamTools' version '1.33'
make[1]: Leaving directory `/«PKGBUILDDIR»'
dh_auto_build
Building Bio-SamTools
-cc -I/usr/include/samtools -I/usr/lib/perl/5.14/CORE -DXS_VERSION="1.32" -DVERSION="1.32" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
+cc -I/usr/include/samtools -I/usr/lib/perl/5.14/CORE -DXS_VERSION="1.33" -DVERSION="1.33" -fPIC -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -Wformat=0 -c -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -g -o lib/Bio/DB/Sam.o lib/Bio/DB/Sam.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/DB/Sam/Sam.bs')
cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o -L/usr/lib -lbam -lz
dh_auto_test
@@ -255,7 +279,7 @@ cc -shared -O2 -g -L/usr/local/lib -fstack-protector -o blib/arch/auto/Bio/DB/Sa
[bam_parse_region] fail to determine the sequence name.
t/01sam.t .. ok
All tests successful.
-Files=1, Tests=112, 1 wallclock secs ( 0.03 usr 0.00 sys + 0.59 cusr 0.04 csys = 0.66 CPU)
+Files=1, Tests=112, 1 wallclock secs ( 0.03 usr 0.02 sys + 0.96 cusr 0.07 csys = 1.08 CPU)
Result: PASS
fakeroot debian/rules binary
dh binary
@@ -265,30 +289,30 @@ dh binary
dh_auto_install
Building Bio-SamTools
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/auto/Bio/DB/Sam/Sam.bs
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/auto/Bio/DB/Sam/Sam.so
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/auto/Bio/DB/Sam/Sam.bs
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Sam.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Pileup.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/ReadIterator.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/PileupWrapper.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Alignment.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Target.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/FetchIterator.pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Query.pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Sam/Constants.pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Sam/SamToGBrowse.pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Sam/Segment.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Query.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/FetchIterator.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Target.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/ReadIterator.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/PileupWrapper.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Alignment.pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/lib/perl5/Bio/DB/Bam/Pileup.pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Sam::Constants.3pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Sam.3pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Query.3pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Target.3pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Pileup.3pm
-Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/bin/genomeCoverageBed.pl
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Sam.3pm
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/share/man/man3/Bio::DB::Bam::Alignment.3pm
Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/bin/bamToGBrowse.pl
+Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/bin/genomeCoverageBed.pl
dh_install
dh_installdocs
dh_installchangelogs
@@ -329,13 +353,13 @@ Installing /«PKGBUILDDIR»/debian/libbio-samtools-perl/usr/bin/bamToGBrowse.pl
dh_gencontrol
dh_md5sums
dh_builddeb
-dpkg-deb: building package `libbio-samtools-perl' in `../libbio-samtools-perl_1.32-1_amd64.deb'.
- dpkg-genchanges >../libbio-samtools-perl_1.32-1_amd64.changes
+dpkg-deb: building package `libbio-samtools-perl' in `../libbio-samtools-perl_1.33-1_amd64.deb'.
+ dpkg-genchanges >../libbio-samtools-perl_1.33-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build libbio-samtools-perl-1.32
+ dpkg-source --after-build libbio-samtools-perl-1.33
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20111123-1633
+Build finished at 20120129-1459
Finished
────────
@@ -347,65 +371,78 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-libbio-samtools-perl_1.32-1_amd64.changes:
+libbio-samtools-perl_1.33-1_amd64.changes:
──────────────────────────────────────────
Format: 1.8
-Date: Wed, 23 Nov 2011 16:26:32 +0900
+Date: Sun, 29 Jan 2012 14:38:27 +0900
Source: libbio-samtools-perl
Binary: libbio-samtools-perl
Architecture: source amd64
-Version: 1.32-1
+Version: 1.33-1
Distribution: unstable
Urgency: low
Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
Changed-By: Charles Plessy <plessy at debian.org>
Description:
- libbio-samtools-perl - read SAM/BAM nucleotide sequence aligment database files
+ libbio-samtools-perl - Perl interface to SamTools library for DNA sequencing
Changes:
- libbio-samtools-perl (1.32-1) unstable; urgency=low
+ libbio-samtools-perl (1.33-1) unstable; urgency=low
+ .
+ * [5fd8406] New upstream release 1.33
+ .
+ [ Nathan Handler ]
+ * [4058f51] Add myself to Uploaders and debian/copyright
+ * [01985a1] Remove version from perl Build-Depend. oldstable has 5.10
+ * [5b63fda] Don't Build-Depend on libmodule-build-perl (included in
+ core since 5.10)
+ * [af3530d] Remove version from libbio-perl-perl Build-Depend. Nothing
+ older in archive
+ * [d6d6dca] Don't Depend on perl, ${perl:Depends} will pull it in
+ * [64ad8db] Turn short description into noun phrase based on abstract
+ in upstream META.json
.
- [36ac64b] New upstream release.
- [dfb9312] Depend on BioPerl 1.6.901, following Upstream.
+ [ Charles Plessy ]
+ * [bb4b659] Renamed debian/upstream-metadata.yaml to debian/upstream.
Checksums-Sha1:
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+ 68a9c89034663597dd89391012980955 332340 perl optional libbio-samtools-perl_1.33.orig.tar.gz
+ 8e370c47251140daa558c25125f6ffee 7345 perl optional libbio-samtools-perl_1.33-1.debian.tar.gz
+ d64f08bf376fd544649ee54dc5de69fc 208410 perl optional libbio-samtools-perl_1.33-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-libbio-samtools-perl_1.32-1_amd64.deb
+libbio-samtools-perl_1.33-1_amd64.deb
─────────────────────────────────────
new debian package, version 2.0.
- size 208154 bytes: control archive= 1621 bytes.
- 1005 bytes, 19 lines control
+ size 208410 bytes: control archive= 1622 bytes.
+ 1002 bytes, 19 lines control
2113 bytes, 28 lines md5sums
Package: libbio-samtools-perl
- Version: 1.32-1
+ Version: 1.33-1
Architecture: amd64
Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
- Installed-Size: 519
- Depends: perl (>= 5.14.2-5), perlapi-5.14.2, libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3.dfsg), libbio-perl-perl (>= 1.6.901)
+ Installed-Size: 520
+ Depends: perl (>= 5.14.2-6), perlapi-5.14.2, libc6 (>= 2.7), zlib1g (>= 1:1.2.3.3.dfsg), libbio-perl-perl (>= 1.6.901)
Enhances: gbrowse, samtools
Section: perl
Priority: optional
Homepage: http://search.cpan.org/dist/Bio-SamTools/
- Description: read SAM/BAM nucleotide sequence aligment database files
+ Description: Perl interface to SamTools library for DNA sequencing
Bio::SamTools provides a Perl interface to the libbam library for indexed and
unindexed SAM/BAM sequence alignment databases. It provides support for
retrieving information on individual alignments, read pairs, and alignment
@@ -415,52 +452,52 @@ libbio-samtools-perl_1.32-1_amd64.deb
allowing BAM files to be used as a backend to the GBrowse genome browser
application.
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/auto/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/auto/Bio/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/auto/Bio/DB/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/auto/Bio/DB/Sam/
--rw-r--r-- root/root 0 2011-11-23 16:33 ./usr/lib/perl5/auto/Bio/DB/Sam/Sam.bs
--rw-r--r-- root/root 260776 2011-11-23 16:33 ./usr/lib/perl5/auto/Bio/DB/Sam/Sam.so
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/Bio/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/
--rw-r--r-- root/root 2453 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/Pileup.pm
--rw-r--r-- root/root 402 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/ReadIterator.pm
--rw-r--r-- root/root 1940 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/PileupWrapper.pm
--rw-r--r-- root/root 17048 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/Alignment.pm
--rw-r--r-- root/root 1046 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/Target.pm
--rw-r--r-- root/root 11084 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm
--rw-r--r-- root/root 335 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/FetchIterator.pm
--rw-r--r-- root/root 4551 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Bam/Query.pm
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Sam/
--rw-r--r-- root/root 2309 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Sam/Constants.pm
--rw-r--r-- root/root 11662 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Sam/SamToGBrowse.pm
--rw-r--r-- root/root 2284 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Sam/Segment.pm
--rw-r--r-- root/root 76399 2011-11-23 16:33 ./usr/lib/perl5/Bio/DB/Sam.pm
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/bin/
--rwxr-xr-x root/root 368 2011-11-23 16:33 ./usr/bin/genomeCoverageBed.pl
--rwxr-xr-x root/root 2244 2011-11-23 16:33 ./usr/bin/bamToGBrowse.pl
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/share/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/share/man/man3/
--rw-r--r-- root/root 20515 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Sam.3pm.gz
--rw-r--r-- root/root 7438 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
--rw-r--r-- root/root 2249 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
--rw-r--r-- root/root 2491 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
--rw-r--r-- root/root 1887 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
--rw-r--r-- root/root 2909 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
--rw-r--r-- root/root 2410 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Sam::Constants.3pm.gz
--rw-r--r-- root/root 2917 2011-11-23 16:33 ./usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-11-23 16:33 ./usr/share/doc/libbio-samtools-perl/
--rw-r--r-- root/root 2899 2011-11-09 07:21 ./usr/share/doc/libbio-samtools-perl/changelog.gz
--rw-r--r-- root/root 10785 2011-11-23 16:23 ./usr/share/doc/libbio-samtools-perl/copyright
--rw-r--r-- root/root 1842 2011-11-23 16:26 ./usr/share/doc/libbio-samtools-perl/changelog.Debian.gz
--rw-r--r-- root/root 242 2011-11-23 16:00 ./usr/share/doc/libbio-samtools-perl/README.Debian
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/Bio/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Sam/
+-rw-r--r-- root/root 2309 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Sam/Constants.pm
+-rw-r--r-- root/root 11662 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Sam/SamToGBrowse.pm
+-rw-r--r-- root/root 2284 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Sam/Segment.pm
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/
+-rw-r--r-- root/root 11161 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/AlignWrapper.pm
+-rw-r--r-- root/root 4551 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/Query.pm
+-rw-r--r-- root/root 335 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/FetchIterator.pm
+-rw-r--r-- root/root 1046 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/Target.pm
+-rw-r--r-- root/root 402 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/ReadIterator.pm
+-rw-r--r-- root/root 1940 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/PileupWrapper.pm
+-rw-r--r-- root/root 17048 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/Alignment.pm
+-rw-r--r-- root/root 2453 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Bam/Pileup.pm
+-rw-r--r-- root/root 76392 2012-01-29 14:59 ./usr/lib/perl5/Bio/DB/Sam.pm
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/auto/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/auto/Bio/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/auto/Bio/DB/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/lib/perl5/auto/Bio/DB/Sam/
+-rw-r--r-- root/root 260776 2012-01-29 14:59 ./usr/lib/perl5/auto/Bio/DB/Sam/Sam.so
+-rw-r--r-- root/root 0 2012-01-29 14:59 ./usr/lib/perl5/auto/Bio/DB/Sam/Sam.bs
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/share/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/share/doc/libbio-samtools-perl/
+-rw-r--r-- root/root 242 2012-01-29 14:12 ./usr/share/doc/libbio-samtools-perl/README.Debian
+-rw-r--r-- root/root 10828 2012-01-29 14:12 ./usr/share/doc/libbio-samtools-perl/copyright
+-rw-r--r-- root/root 2959 2011-12-07 06:15 ./usr/share/doc/libbio-samtools-perl/changelog.gz
+-rw-r--r-- root/root 2133 2012-01-29 14:44 ./usr/share/doc/libbio-samtools-perl/changelog.Debian.gz
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/share/man/man3/
+-rw-r--r-- root/root 2493 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::AlignWrapper.3pm.gz
+-rw-r--r-- root/root 7439 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::Alignment.3pm.gz
+-rw-r--r-- root/root 2251 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::PileupWrapper.3pm.gz
+-rw-r--r-- root/root 2411 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Sam::Constants.3pm.gz
+-rw-r--r-- root/root 2910 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::Pileup.3pm.gz
+-rw-r--r-- root/root 20518 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Sam.3pm.gz
+-rw-r--r-- root/root 1890 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::Target.3pm.gz
+-rw-r--r-- root/root 2919 2012-01-29 14:59 ./usr/share/man/man3/Bio::DB::Bam::Query.3pm.gz
+drwxr-xr-x root/root 0 2012-01-29 14:59 ./usr/bin/
+-rwxr-xr-x root/root 2244 2012-01-29 14:59 ./usr/bin/bamToGBrowse.pl
+-rwxr-xr-x root/root 368 2012-01-29 14:59 ./usr/bin/genomeCoverageBed.pl
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -484,74 +521,25 @@ I: Lintian run was successful.
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- debhelper* file* gettext* gettext-base* groff-base* html2text*
- intltool-debian* libbam-dev* libbio-perl-perl* libcroco3* libdata-stag-perl*
- libffi5* libglib2.0-0* libio-string-perl* libmagic1* libpcre3* libpipeline1*
- libunistring0* libxml2* man-db* po-debconf*
- sbuild-build-depends-libbio-samtools-perl-dummy* zlib1g-dev*
-0 upgraded, 0 newly installed, 23 to remove and 0 not upgraded.
-After this operation, 46.4 MB disk space will be freed.
-(Reading database ... 14112 files and directories currently installed.)
-Removing sbuild-build-depends-libbio-samtools-perl-dummy ...
-Removing debhelper ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libbam-dev ...
-Removing libbio-perl-perl ...
-Removing libcroco3 ...
-Purging configuration files for libcroco3 ...
-Removing libdata-stag-perl ...
-Removing libglib2.0-0 ...
-Purging configuration files for libglib2.0-0 ...
-Removing libffi5 ...
-Purging configuration files for libffi5 ...
-Removing libio-string-perl ...
-Removing libmagic1 ...
-Purging configuration files for libmagic1 ...
-Removing libpcre3 ...
-Purging configuration files for libpcre3 ...
-Removing libpipeline1 ...
-Purging configuration files for libpipeline1 ...
-Removing libunistring0 ...
-Purging configuration files for libunistring0 ...
-Removing libxml2 ...
-Purging configuration files for libxml2 ...
-Removing zlib1g-dev ...
+Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 3116
-Build-Time: 6
+Build-Space: 3156
+Build-Time: 11
Distribution: unstable
-Install-Time: 29
-Job: libbio-samtools-perl_1.32-1.dsc
+Install-Time: 37
+Job: libbio-samtools-perl_1.33-1.dsc
Lintian: pass
Package: libbio-samtools-perl
-Package-Time: 39
-Source-Version: 1.32-1
-Space: 3116
+Package-Time: 54
+Source-Version: 1.33-1
+Space: 3156
Status: successful
-Version: 1.32-1
+Version: 1.33-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20111123-1633
-Build needed 00:00:39, 3116k disc space
+Finished at 20120129-1459
+Build needed 00:00:54, 3156k disc space
diff --git a/dsc b/dsc
index 3075dd6..0b3dbf2 100644
--- a/dsc
+++ b/dsc
@@ -5,40 +5,40 @@ Format: 3.0 (quilt)
Source: libbio-samtools-perl
Binary: libbio-samtools-perl
Architecture: any
-Version: 1.32-1
+Version: 1.33-1
Maintainer: Debian Perl Group <pkg-perl-maintainers at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>, Nathan Handler <nhandler at ubuntu.com>
Homepage: http://search.cpan.org/dist/Bio-SamTools/
Standards-Version: 3.9.2
Vcs-Browser: http://git.debian.org/?p=pkg-perl/packages/libbio-samtools-perl.git
Vcs-Git: git://git.debian.org/git/pkg-perl/packages/libbio-samtools-perl.git
-Build-Depends: debhelper (>= 8), libmodule-build-perl, perl-modules, perl (>= 5.8), zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl (>= 1.6.901)
+Build-Depends: debhelper (>= 8), perl, zlib1g-dev, libbam-dev (>= 0.1.16-1~), libbio-perl-perl
Package-List:
libbio-samtools-perl deb perl optional
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+=7VzX
-----END PGP SIGNATURE-----
--
read SAM/BAM nucleotide sequence aligment database files
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