[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.14-1-5-gd46ae92
Charles Plessy
plessy at debian.org
Mon Jul 11 12:22:00 UTC 2011
The following commit has been merged in the meta branch:
commit d46ae92b9187808b67ef826cb9537e95aa3a389c
Author: Charles Plessy <plessy at debian.org>
Date: Mon Jul 11 21:20:11 2011 +0900
Uploaded samtools_0.1.17-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index d5ffd53..6d14215 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,46 +14,47 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- 42c68b748cd4379a7cf733829f96e72b5bf93fa4 1939 samtools_0.1.16-1.dsc
- 4f00dad58f707efb84a4d0144b6245e4da4077e5 379809 samtools_0.1.16.orig.tar.bz2
- abed22d9f1f442efa09bddb45ad442aa3f1d6e91 7161 samtools_0.1.16-1.debian.tar.gz
- 7c5f8117b1b262c9387aef350e375a4f15e7f811 602354 samtools_0.1.16-1_amd64.deb
- dae61375b51af04266dbf80de13f9b9e0ccacb46 171096 libbam-dev_0.1.16-1_amd64.deb
+ fc51cf7dab0f0b9460365430dcc78a3f3a3a355b 1946 samtools_0.1.17-1.dsc
+ 4d2ef4273d9f71cd1f504f43c596970845d78718 373930 samtools_0.1.17.orig.tar.bz2
+ 8b5a95897b302b2433141da51e23bd0a7bb10634 7643 samtools_0.1.17-1.debian.tar.gz
+ 91e3412989cbdc4cd85acaa95f3b07967ba9fea5 592564 samtools_0.1.17-1_amd64.deb
+ 71b92830ec7836f06f537582301764a77a00dda7 170236 libbam-dev_0.1.17-1_amd64.deb
Checksums-Sha256:
- c3e304bfd7c931cf256cc34556892b3edfd7a60dea78123b868f0dd8ab613130 1939 samtools_0.1.16-1.dsc
- ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726 379809 samtools_0.1.16.orig.tar.bz2
- ccdae2d562a2cb58e2b68e37dc1cbc7aca49f9d79415cf51fabc7a7b1d37af9f 7161 samtools_0.1.16-1.debian.tar.gz
- 79be8a4cbbacd7b9ff87afba0957030b375d6b84f5a93aa5f5c7b259b0f4b0aa 602354 samtools_0.1.16-1_amd64.deb
- f25fb6eba596d2dbd706afb60e286dabb0a047092ae4d592f764e30160d0da28 171096 libbam-dev_0.1.16-1_amd64.deb
+ 488547066eda9964112d1428e45fc02bbc58cc58d4b43d6ad3b37b49a802ebcd 1946 samtools_0.1.17-1.dsc
+ aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e 373930 samtools_0.1.17.orig.tar.bz2
+ d13d2d8257a52154c0159cad5efdc596657a3503cfc8bcc31f7649771019c9d8 7643 samtools_0.1.17-1.debian.tar.gz
+ 51174153f98b9db1b2f3b19467d12ceb57042b9186da5abaf213a9374a86d6e6 592564 samtools_0.1.17-1_amd64.deb
+ d7ee2884b2e6ed7afa68be9c0fbf7e3d484394180e8ce8b9d9062a5cb8ece403 170236 libbam-dev_0.1.17-1_amd64.deb
Files:
- 6d598975c4cdf12a8bc6cb6def6eb74a 1939 science optional samtools_0.1.16-1.dsc
- ae26c63a783f95a45ddf8a109c9d9a5d 379809 science optional samtools_0.1.16.orig.tar.bz2
- 1a535f5525a4a813346b611b1f9d8b19 7161 science optional samtools_0.1.16-1.debian.tar.gz
- a69b4367f38d9bc907012286bfc315b2 602354 science optional samtools_0.1.16-1_amd64.deb
- 4f422b35737c90619178078f54531218 171096 libdevel optional libbam-dev_0.1.16-1_amd64.deb
+ d797413912df8d79168fb7dde1302d6f 1946 science optional samtools_0.1.17-1.dsc
+ 9549f7a6bba894766df9c3dd18d61f0b 373930 science optional samtools_0.1.17.orig.tar.bz2
+ 2167f175122970511b8de75e59fb1ad0 7643 science optional samtools_0.1.17-1.debian.tar.gz
+ da5b86a1225e99de2751bf4020ff1e73 592564 science optional samtools_0.1.17-1_amd64.deb
+ f6491566d491aece7298f00cb5c8867c 170236 libdevel optional libbam-dev_0.1.17-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 69e851c..7863cc8 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,17 +1,18 @@
-sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on anx191
+sbuild (Debian sbuild) 0.62.4 (25 Jun 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.16-1 (amd64) 19 mai 2011 13:24 ║
+║ samtools 0.1.17-1 (amd64) 11 Jul 2011 21:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.16-1
-Source Version: 0.1.16-1
+Version: 0.1.17-1
+Source Version: 0.1.17-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/samtools-5c5WTK' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-5ead40fa-e240-4c4b-a1e3-84085e738504' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-FnIeBX/samtools-0.1.17' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-FnIeBX' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-0cfd274e-a0bf-4e81-8a7b-40093fcd29f0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -20,9 +21,6 @@ I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-5e
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 http://ftp.riken.jp sid InRelease
-Hit http://ftp.riken.jp sid/main amd64 Packages/DiffIndex
-Hit http://ftp.riken.jp sid/main TranslationIndex
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -37,14 +35,14 @@ Reading state information...
Local sources
─────────────
-samtools_0.1.16-1.dsc exists in .; copying to chroot
+samtools_0.1.17-1.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-EDTXTU/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-OkL_5I/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/702 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 ... 10783 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), cdbs, libncurses5-dev, zlib1g-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), debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-gHdSaO/apt_archive/sbuild-build-depends-samtools-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), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-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), debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-oHnVWg/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
@@ -81,31 +71,29 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl
+ devscripts dh-make gettext-doc groff ncurses-doc less www-browser
+ libmail-box-perl procmail graphviz
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
The following NEW packages will be installed:
- bsdmainutils cdbs debhelper file gettext gettext-base groff-base html2text
+ cdbs debhelper diffstat file gettext gettext-base groff-base html2text
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
- libpipeline1 libunistring0 libxml2 man-db po-debconf
+ libpipeline1 libunistring0 libxml2 man-db po-debconf quilt
sbuild-build-depends-samtools-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/9983 kB of archives.
-After this operation, 29.5 MB of additional disk space will be used.
-Selecting previously deselected package bsdmainutils.
-(Reading database ... 10783 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.2.2_amd64.deb) ...
-Selecting previously deselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.21-5_amd64.deb) ...
+0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
+Need to get 0 B/10.2 MB of archives.
+After this operation, 29.7 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_amd64.deb) ...
+(Reading database ... 11027 files and directories currently installed.)
+Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
+Selecting previously deselected package groff-base.
+Unpacking groff-base (from .../groff-base_1.21-6_amd64.deb) ...
Selecting previously deselected package man-db.
Unpacking man-db (from .../man-db_2.6.0.2-1_amd64.deb) ...
Selecting previously deselected package libmagic1.
@@ -117,7 +105,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.12-3_amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -133,27 +121,28 @@ Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) .
Selecting previously deselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
-Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.0_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Selecting previously deselected package diffstat.
+Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_amd64.deb) ...
+Selecting previously deselected package quilt.
+Unpacking quilt (from .../archives/quilt_0.48-7_all.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
Selecting previously deselected package sbuild-build-depends-samtools-dummy.
Unpacking sbuild-build-depends-samtools-dummy (from .../sbuild-build-depends-samtools-dummy.deb) ...
-Setting up bsdmainutils (8.2.2) ...
-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 (1.21-5) ...
-Setting up libpipeline1 (1.2.0-1) ...
+Setting up libpipeline1 (1.2.0-3) ...
+Setting up groff-base (1.21-6) ...
Setting up man-db (2.6.0.2-1) ...
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 libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-2+b1) ...
+Setting up libxml2 (2.7.8.dfsg-3) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
@@ -162,9 +151,11 @@ Setting up libunistring0 (0.9.3-4) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.1.6) ...
-Setting up cdbs (0.4.93) ...
+Setting up debhelper (8.9.0) ...
+Setting up cdbs (0.4.94) ...
+Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
+Setting up quilt (0.48-7) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
@@ -173,8 +164,8 @@ Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.51.20110421-5 dpkg-dev_1.16.0.3 g++-4.6_4.6.0-7 gcc-4.6_4.6.0-7 libc6-dev_2.13-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 linux-libc-dev_2.6.38-5
-Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.51.20110421-5 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.93 coreutils_8.5-1 cpp_4:4.6.0-5 cpp-4.6_4.6.0-7 dash_0.5.5.1-7.4 debconf_1.5.39 debconf-i18n_1.5.39 debfoster_2.7-1.1 debhelper_8.1.6 debian-archive-keyring_2010.08.28 debianutils_4 diffutils_1:3.0-1 dpkg_1.16.0.3 dpkg-dev_1.16.0.3 e2fslibs_1.41.12-4 e2fsprogs_1.41.12-4 fakeroot_1.15.1-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.0-5 g++-4.6_4.6.0-7 gcc_4:4.6.0-5 gcc-4.6_4.6.0-7 gcc-4.6-base_4.6.0-7 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.6.3-3 groff-base_1.21-5 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.6 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-9.1 libbz2-1.0_1.0.5-6 libc-bin_2.13-4 libc-dev-bin_2.13-4 libc6_2.13-4 libc6-dev_2.13-4 libclass-isa-perl_0.36-1 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-4 libcroco3_0.6.2-1 libdb4.7_4.7.25-19 libdb4.8_4.8.30-8 libdb5.1_5.1.25-10 libdpkg-perl_1.16.0.3 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-7 libgdbm3_1.8.3-9 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-7 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmpc2_0.9-3 libmpfr4_3.0.1-3 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-3 libpam-runtime_1.1.2-3 libpam0g_1.1.2-3 libpcre3_8.12-3 libpipeline1_1.2.0-1 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libquadmath0_4.6.0-7 libreadline6_6.2-2 libselinux1_2.0.98-1+b1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.41.12-4 libstdc++6_4.6.0-7 libstdc++6-4.6-dev_4.6.0-7 libswitch-perl_2.16-1 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2+b1 linux-libc-dev_2.6.38-5 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.17.2-9.1 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-1 perl_5.12.3-6 perl-base_5.12.3-6 perl-modules_5.12.3-6 po-debconf_1.0.16+nmu1 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.6 sysvinit_2.88dsf-13.6 sysvinit-utils_2.88dsf-13.6 tar_1.25-3 tzdata_2011g-1 util-linux_2.17.2-9.1 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.21.52.20110707-1 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-3 gcc-4.6_4.6.1-3 libc6-dev_2.13-10 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 linux-libc-dev_2.6.39-3
+Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.52.20110707-1 bsdmainutils_8.2.3 bsdutils_1:2.19.1-2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.94 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-3 dash_0.5.5.1-7.4 debconf_1.5.40 debconf-i18n_1.5.40 debfoster_2.7-1.1 debhelper_8.9.0 debian-archive-keyring_2010.08.28 debianutils_4.0.2 diffstat_1.54-1 diffutils_1:3.0-1 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 g++_4:4.6.1-2 g++-4.6_4.6.1-3 gcc_4:4.6.1-2 gcc-4.6_4.6.1-3 gcc-4.6-base_4.6.1-3 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.8-2 groff-base_1.21-6 gzip_1.3.12-9 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.10 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-2 libattr1_1:2.4.46-2 libblkid1_2.19.1-2 libbz2-1.0_1.0.5-6 libc-bin_2.13-10 libc-dev-bin_2.13-10 libc6_2.13-10 libc6-dev_2.13-10 libclass-isa-perl_0.36-1 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-3 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.1-3 libgpm2_1.20.4-3.4 liblocale-gettext-perl_1.05-6+b1 liblzma2_5.0.0-2 libmagic1_5.04-5+b1 libmount1_2.19.1-2 libmpc2_0.9-3 libmpfr4_3.0.1-4 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 libpcre3_8.12-3 libpipeline1_1.2.0-3 libpng12-0_1.2.44-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-3 libreadline6_6.2-2 libselinux1_2.0.98-1.1 libsepol1_2.0.42-1 libslang2_2.2.4-2 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-3 libstdc++6-4.6-dev_4.6.1-3 libswitch-perl_2.16-1 libtext-charwidth-perl_0.04-6+b1 libtext-iconv-perl_1.7-2+b1 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-17 libuuid1_2.19.1-2 libxml2_2.7.8.dfsg-3 linux-libc-dev_2.6.39-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.2-1 mawk_1.3.3-15 mount_2.19.1-2 multiarch-support_2.13-10 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-1 perl-base_5.12.4-1 perl-modules_5.12.4-1 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-2 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.1-9 sensible-utils_0.0.6 sysv-rc_2.88dsf-13.10 sysvinit_2.88dsf-13.10 sysvinit-utils_2.88dsf-13.10 tar_1.25-3 tzdata_2011h-3 util-linux_2.19.1-2 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -184,16 +175,35 @@ Package versions: apt_0.8.14.1 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (samtools_0.1.16-1.dsc)
-dpkg-source: info: extracting samtools in samtools-0.1.16
-dpkg-source: info: unpacking samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.16-1.debian.tar.gz
+dpkg-source: warning: extracting unsigned source package (samtools_0.1.17-1.dsc)
+dpkg-source: info: extracting samtools in samtools-0.1.17
+dpkg-source: info: unpacking samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: applying no-pileup-tests.patch
Check disc space
────────────────
Sufficient free space for build
+User Environment
+────────────────
+
+HOME=/sbuild-nonexistent
+LOGNAME=charles
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1000
+SCHROOT_GROUP=charles
+SCHROOT_SESSION_ID=sid-amd64-sbuild-0cfd274e-a0bf-4e81-8a7b-40093fcd29f0
+SCHROOT_UID=31051
+SCHROOT_USER=charles
+SHELL=/bin/sh
+TERM=xterm
+USER=charles
+USERNAME=charles
+
dpkg-buildpackage
─────────────────
@@ -203,41 +213,67 @@ 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 samtools
-dpkg-buildpackage: source version 0.1.16-1
+dpkg-buildpackage: source version 0.1.17-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.16
+ dpkg-source --before-build samtools-0.1.17
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
dh_testroot
rm -f debian/stamp-makefile-build debian/stamp-makefile-install
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/misc'
-make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
rm -f debian/stamp-makefile-check
dh_clean
+/usr/bin/make -f debian/rules reverse-config
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+if [ -d "." ]; then \
+ cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
+ fi
+Removing patch no-pileup-tests.patch
+Restoring examples/Makefile
+
+No patches applied
+rm -rf ./.pc
+rm -f debian/stamp-patch*
rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- dpkg-source -b samtools-0.1.16
+ dpkg-source -b samtools-0.1.17
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_0.1.16.orig.tar.bz2
-dpkg-source: info: building samtools in samtools_0.1.16-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.16-1.dsc
+dpkg-source: warning: patches have not been applied, applying them now (use --no-preparation to override)
+dpkg-source: info: applying no-pileup-tests.patch
+dpkg-source: info: building samtools using existing ./samtools_0.1.17.orig.tar.bz2
+dpkg-source: info: building samtools in samtools_0.1.17-1.debian.tar.gz
+dpkg-source: info: building samtools in samtools_0.1.17-1.dsc
debian/rules build
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
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `reverse-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
+cd . && QUILT_PATCHES=/«PKGBUILDDIR»/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
+File series fully applied, ends at patch no-pileup-tests.patch
+touch debian/stamp-patched
+/usr/bin/make -f debian/rules update-config
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[1]: Nothing to be done for `update-config'.
+make[1]: Leaving directory `/«PKGBUILDDIR»'
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
+make[1]: Entering directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
bgzf.c: In function 'bgzf_close':
bgzf.c:630:8: warning: variable 'count' set but not used [-Wunused-but-set-variable]
@@ -252,7 +288,6 @@ bam_pileup.c: In function 'resolve_cigar2':
bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. glf.c -o glf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
@@ -266,28 +301,28 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
kprobaln.c: In function 'kpa_glocal':
kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -cru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/misc'
+ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
@@ -306,25 +341,25 @@ cut_target.c: In function 'main_cut_target':
cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.16'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Entering directory `/«PKGBUILDDIR»'
+make[3]: Entering directory `/«PKGBUILDDIR»'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/«PKGBUILDDIR»'
+make[3]: Entering directory `/«PKGBUILDDIR»/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[3]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[3]: Entering directory `/«PKGBUILDDIR»/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/misc'
-gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+make[3]: Leaving directory `/«PKGBUILDDIR»/misc'
+gcc -g -O2 -g -O2 -Wall -fPIC -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
+make[2]: Leaving directory `/«PKGBUILDDIR»'
+make[2]: Entering directory `/«PKGBUILDDIR»/bcftools'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -O2 -Wall -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/bcftools'
+make[2]: Entering directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -334,19 +369,17 @@ gcc -g -O2 -g -O2 -Wall -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -O2 -Wall -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -O2 -Wall -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
+make[1]: Leaving directory `/«PKGBUILDDIR»'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -Wall -fPIC" CXXFLAGS="-g -O2 -g -O2 -Wall" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.16/examples'
+make[1]: Entering directory `/«PKGBUILDDIR»/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
-../samtools pileup -gf ex1.fa ex1.bam > ex1.glf
-../samtools pileup -cf ex1.fa ex1.bam | gzip > ex1.pileup.gz
../samtools index ex1.bam
../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
[samopen] SAM header is present: 2 sequences.
@@ -362,7 +395,6 @@ make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.16/examples'
../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools glfview ex1.glf | gzip > ex1.glfview.gz
../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
@@ -370,7 +402,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/examples'
+make[1]: Leaving directory `/«PKGBUILDDIR»/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary
test -x debian/rules
@@ -397,7 +429,6 @@ dh_installcatalogs -psamtools
dh_installpam -psamtools
dh_installlogrotate -psamtools
dh_installlogcheck -psamtools
-dh_installgsettings -psamtools
dh_installchangelogs -psamtools ./ChangeLog
dh_installudev -psamtools
dh_lintian -psamtools
@@ -405,7 +436,9 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /«BUILDDIR»/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
+dh_installgsettings -psamtools
+install -m 644 bcftools/README /«PKGBUILDDIR»/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /«PKGBUILDDIR»/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -419,7 +452,6 @@ dh_installcatalogs -plibbam-dev
dh_installpam -plibbam-dev
dh_installlogrotate -plibbam-dev
dh_installlogcheck -plibbam-dev
-dh_installgsettings -plibbam-dev
dh_installchangelogs -plibbam-dev ./ChangeLog
dh_installudev -plibbam-dev
dh_lintian -plibbam-dev
@@ -427,11 +459,12 @@ dh_bugfiles -plibbam-dev
dh_install -plibbam-dev
dh_link -plibbam-dev
dh_installmime -plibbam-dev
+dh_installgsettings -plibbam-dev
dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«BUILDDIR»/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«PKGBUILDDIR»/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -446,18 +479,18 @@ dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
dh_builddeb -psamtools -- -Z=bzip2
-dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.17-1_amd64.deb'.
dh_gencontrol -plibbam-dev
dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
dh_md5sums -plibbam-dev
dh_builddeb -plibbam-dev -- -Z=bzip2
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.16-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.16-1_amd64.changes
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.17-1_amd64.deb'.
+ dpkg-genchanges >../samtools_0.1.17-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.16
+ dpkg-source --after-build samtools-0.1.17
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110519-1325
+Build finished at 20110711-2107
Finished
────────
@@ -469,15 +502,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_amd64.changes:
+samtools_0.1.17-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Thu, 19 May 2011 13:24:25 +0900
+Date: Mon, 11 Jul 2011 21:04:30 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.16-1
+Version: 0.1.17-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -485,49 +518,50 @@ Changed-By: Charles Plessy <plessy at debian.org>
Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
-Closes: 625622 626044
Changes:
- samtools (0.1.16-1) unstable; urgency=low
+ samtools (0.1.17-1) unstable; urgency=low
.
- * New upstream release, implementing SAM Spec v1.4.
- * Distribute sam.h and the other headers in /usr/include/samtools.
- Closes: #625622, #626044, LP: #690997.
+ * New upstream release 0.1.17 (6 July, 2011).
+ * bcftools.1 and samtools.1 merged (debian/rules, debian/samtools.manpages).
+ * Patched the example makefile to not use samtools pileup, deprecated.
+ (debian/control, debian/rules, debian/patches/series,
+ debian/patches/no-pileup-tests.patch)
Checksums-Sha1:
- ea832d79025c2b11bb604e9c0de4ddcc1a888847 1053 samtools_0.1.16-1.dsc
- 4f00dad58f707efb84a4d0144b6245e4da4077e5 379809 samtools_0.1.16.orig.tar.bz2
- abed22d9f1f442efa09bddb45ad442aa3f1d6e91 7161 samtools_0.1.16-1.debian.tar.gz
- 7c5f8117b1b262c9387aef350e375a4f15e7f811 602354 samtools_0.1.16-1_amd64.deb
- dae61375b51af04266dbf80de13f9b9e0ccacb46 171096 libbam-dev_0.1.16-1_amd64.deb
+ 18c7ddc02f6862a0302e1ef8352a3c1666324424 1060 samtools_0.1.17-1.dsc
+ 4d2ef4273d9f71cd1f504f43c596970845d78718 373930 samtools_0.1.17.orig.tar.bz2
+ 8b5a95897b302b2433141da51e23bd0a7bb10634 7643 samtools_0.1.17-1.debian.tar.gz
+ 91e3412989cbdc4cd85acaa95f3b07967ba9fea5 592564 samtools_0.1.17-1_amd64.deb
+ 71b92830ec7836f06f537582301764a77a00dda7 170236 libbam-dev_0.1.17-1_amd64.deb
Checksums-Sha256:
- 3b9ced0b181f7579bc46afc956bf34c97af915efb361233f3f1462432207602a 1053 samtools_0.1.16-1.dsc
- ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726 379809 samtools_0.1.16.orig.tar.bz2
- ccdae2d562a2cb58e2b68e37dc1cbc7aca49f9d79415cf51fabc7a7b1d37af9f 7161 samtools_0.1.16-1.debian.tar.gz
- 79be8a4cbbacd7b9ff87afba0957030b375d6b84f5a93aa5f5c7b259b0f4b0aa 602354 samtools_0.1.16-1_amd64.deb
- f25fb6eba596d2dbd706afb60e286dabb0a047092ae4d592f764e30160d0da28 171096 libbam-dev_0.1.16-1_amd64.deb
+ 4f036a06099512e41d848cbbe7c93191580bb0b0cedeecfa91e36c6d84a2105e 1060 samtools_0.1.17-1.dsc
+ aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e 373930 samtools_0.1.17.orig.tar.bz2
+ d13d2d8257a52154c0159cad5efdc596657a3503cfc8bcc31f7649771019c9d8 7643 samtools_0.1.17-1.debian.tar.gz
+ 51174153f98b9db1b2f3b19467d12ceb57042b9186da5abaf213a9374a86d6e6 592564 samtools_0.1.17-1_amd64.deb
+ d7ee2884b2e6ed7afa68be9c0fbf7e3d484394180e8ce8b9d9062a5cb8ece403 170236 libbam-dev_0.1.17-1_amd64.deb
Files:
- c7c4a3dd95f48c273226468ca968188e 1053 science optional samtools_0.1.16-1.dsc
- ae26c63a783f95a45ddf8a109c9d9a5d 379809 science optional samtools_0.1.16.orig.tar.bz2
- 1a535f5525a4a813346b611b1f9d8b19 7161 science optional samtools_0.1.16-1.debian.tar.gz
- a69b4367f38d9bc907012286bfc315b2 602354 science optional samtools_0.1.16-1_amd64.deb
- 4f422b35737c90619178078f54531218 171096 libdevel optional libbam-dev_0.1.16-1_amd64.deb
+ 4ea7e31c3eddd9ec6527a91cadebc594 1060 science optional samtools_0.1.17-1.dsc
+ 9549f7a6bba894766df9c3dd18d61f0b 373930 science optional samtools_0.1.17.orig.tar.bz2
+ 2167f175122970511b8de75e59fb1ad0 7643 science optional samtools_0.1.17-1.debian.tar.gz
+ da5b86a1225e99de2751bf4020ff1e73 592564 science optional samtools_0.1.17-1_amd64.deb
+ f6491566d491aece7298f00cb5c8867c 170236 libdevel optional libbam-dev_0.1.17-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.16-1_amd64.deb
+samtools_0.1.17-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 602354 bytes: control archive= 1788 bytes.
+ size 592564 bytes: control archive= 1761 bytes.
786 bytes, 16 lines control
- 2520 bytes, 38 lines md5sums
+ 2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1092
+ Installed-Size: 1068
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -540,23 +574,23 @@ samtools_0.1.16-1_amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/lib/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/lib/samtools/
--rwxr-xr-x root/root 11920 2011-05-19 13:25 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 19272 2011-05-19 13:25 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8648 2011-05-19 13:25 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 8032 2011-05-19 13:25 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8096 2011-05-19 13:25 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/bin/
--rwxr-xr-x root/root 384280 2011-05-19 13:25 ./usr/bin/samtools
--rwxr-xr-x root/root 24496 2011-05-19 13:25 ./usr/bin/razip
--rwxr-xr-x root/root 126376 2011-05-19 13:25 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/lib/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11960 2011-07-11 21:07 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 19288 2011-07-11 21:07 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8688 2011-07-11 21:07 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 8080 2011-07-11 21:07 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8144 2011-07-11 21:07 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/bin/
+-rwxr-xr-x root/root 356952 2011-07-11 21:07 ./usr/bin/samtools
+-rwxr-xr-x root/root 24400 2011-07-11 21:07 ./usr/bin/razip
+-rwxr-xr-x root/root 130528 2011-07-11 21:07 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/samtools/
-rwxr-xr-x root/root 18572 2011-03-22 12:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-05-19 13:25 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-07-11 21:07 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 4996 2010-11-17 13:16 ./usr/share/samtools/interpolate_sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 13:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 13:16 ./usr/share/samtools/psl2sam.pl
@@ -564,47 +598,47 @@ drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 13:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 7881 2010-11-17 13:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 14299 2010-11-17 13:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 15437 2011-03-02 04:50 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 15707 2011-07-07 11:59 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 2415 2010-11-17 13:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 13:16 ./usr/share/samtools/wgsim_eval.pl
-rwxr-xr-x root/root 5989 2010-11-17 13:16 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/man/man1/
--rw-r--r-- root/root 2101 2011-05-19 13:25 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-05-19 13:25 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8438 2011-05-19 13:25 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/samtools/examples/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-07-11 21:07 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-07-11 21:07 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 3225 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 114565 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 786 2011-04-22 12:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-05-19 13:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-07-11 21:07 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 886 2010-11-17 13:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 12:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 9930 2011-07-07 11:59 ./usr/share/doc/samtools/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 13:20 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1966 2011-05-19 13:25 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1462 2011-05-19 13:24 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1031 2011-05-19 13:20 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-05-19 13:20 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 5371 2011-07-11 20:19 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2011-07-11 21:07 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1573 2011-07-11 21:04 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1031 2011-05-20 18:55 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-05-20 18:55 ./usr/share/doc/samtools/reference
+lrwxrwxrwx root/root 0 2011-07-11 21:07 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.16-1_amd64.deb
+libbam-dev_0.1.17-1_amd64.deb
─────────────────────────────
new debian package, version 2.0.
- size 171096 bytes: control archive= 928 bytes.
+ size 170236 bytes: control archive= 927 bytes.
674 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.16-1
+ Version: 0.1.17-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 484
+ Installed-Size: 476
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -615,25 +649,25 @@ libbam-dev_0.1.16-1_amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/lib/
--rw-r--r-- root/root 328218 2011-05-19 13:25 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/include/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/include/samtools/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/lib/
+-rw-r--r-- root/root 320058 2011-07-11 21:07 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/include/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/include/samtools/
-rw-r--r-- root/root 17815 2011-03-02 04:50 ./usr/include/samtools/khash.h
-rw-r--r-- root/root 3188 2010-11-17 13:16 ./usr/include/samtools/faidx.h
-rw-r--r-- root/root 4617 2011-04-11 07:33 ./usr/include/samtools/bgzf.h
-rw-r--r-- root/root 2625 2010-11-17 13:16 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 24548 2011-04-22 12:16 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 24548 2011-07-07 11:59 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/doc/libbam-dev/
-rw-r--r-- root/root 33578 2011-03-02 04:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9373 2011-04-22 12:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9930 2011-07-07 11:59 ./usr/share/doc/libbam-dev/NEWS.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5392 2011-05-19 13:20 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1462 2011-05-19 13:24 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-rw-r--r-- root/root 5371 2011-07-11 20:19 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1573 2011-07-11 21:04 ./usr/share/doc/libbam-dev/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -641,11 +675,33 @@ drwxr-xr-x root/root 0 2011-05-19 13:25 ./usr/share/doc/libbam-dev/
└──────────────────────────────────────────────────────────────────────────────┘
+lintian
+───────
+
+P: samtools source: unneeded-build-dep-on-quilt
+I: samtools source: quilt-patch-missing-description no-pileup-tests.patch
+W: samtools source: debian-watch-file-should-use-sf-redirector line 4
+W: samtools: manpage-has-errors-from-man usr/share/man/man1/samtools.1.gz around line 725: table wider than line width
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:9
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:23
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:25
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:33
+I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:58
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:59
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:317
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:327
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:334
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:351
+I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 26 more occurrences not shown
+
+I: Lintian run was successful.
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /«CHROOT»/«BUILDDIR»
+Purging /«BUILDDIR»
Reading package lists...
Building dependency tree...
Reading state information...
@@ -654,26 +710,26 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bsdmainutils* cdbs* debhelper* file* gettext* gettext-base* groff-base*
+ cdbs* debhelper* diffstat* file* gettext* gettext-base* groff-base*
html2text* intltool-debian* libcroco3* libglib2.0-0* libmagic1*
libncurses5-dev* libpcre3* libpipeline1* libunistring0* libxml2* man-db*
- po-debconf* sbuild-build-depends-core-dummy*
- sbuild-build-depends-samtools-dummy* zlib1g-dev*
+ po-debconf* quilt* sbuild-build-depends-samtools-dummy* zlib1g-dev*
0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
-After this operation, 29.5 MB disk space will be freed.
-(Reading database ... 12221 files and directories currently installed.)
+After this operation, 29.7 MB disk space will be freed.
+(Reading database ... 12442 files and directories currently installed.)
Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
+Removing quilt ...
+Purging configuration files for quilt ...
+Removing diffstat ...
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 ...
@@ -693,7 +749,6 @@ Removing libunistring0 ...
Purging configuration files for libunistring0 ...
Removing libxml2 ...
Purging configuration files for libxml2 ...
-Removing sbuild-build-depends-core-dummy ...
Removing zlib1g-dev ...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -701,17 +756,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12588
+Build-Space: 12220
Build-Time: 23
Distribution: unstable
-Install-Time: 26
-Job: samtools_0.1.16-1.dsc
+Install-Time: 27
+Job: samtools_0.1.17-1.dsc
+Lintian: pass
Package: samtools
-Package-Time: 56
-Source-Version: 0.1.16-1
-Space: 12588
+Package-Time: 53
+Source-Version: 0.1.17-1
+Space: 12220
Status: successful
-Version: 0.1.16-1
+Version: 0.1.17-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110519-1325
-Build needed 00:00:56, 12588k disc space
+Finished at 20110711-2107
+Build needed 00:00:53, 12220k disc space
diff --git a/dsc b/dsc
index dc55d23..f74ec89 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, libbam-dev
Architecture: any
-Version: 0.1.16-1
+Version: 0.1.17-1
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 +13,31 @@ Homepage: http://samtools.sourceforge.net
Standards-Version: 3.9.2
Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git
Vcs-Git: git://git.debian.org/debian-med/samtools.git
-Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, quilt, libncurses5-dev, zlib1g-dev
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- abed22d9f1f442efa09bddb45ad442aa3f1d6e91 7161 samtools_0.1.16-1.debian.tar.gz
+ 4d2ef4273d9f71cd1f504f43c596970845d78718 373930 samtools_0.1.17.orig.tar.bz2
+ 8b5a95897b302b2433141da51e23bd0a7bb10634 7643 samtools_0.1.17-1.debian.tar.gz
Checksums-Sha256:
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- ccdae2d562a2cb58e2b68e37dc1cbc7aca49f9d79415cf51fabc7a7b1d37af9f 7161 samtools_0.1.16-1.debian.tar.gz
+ aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e 373930 samtools_0.1.17.orig.tar.bz2
+ d13d2d8257a52154c0159cad5efdc596657a3503cfc8bcc31f7649771019c9d8 7643 samtools_0.1.17-1.debian.tar.gz
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- 1a535f5525a4a813346b611b1f9d8b19 7161 samtools_0.1.16-1.debian.tar.gz
+ 9549f7a6bba894766df9c3dd18d61f0b 373930 samtools_0.1.17.orig.tar.bz2
+ 2167f175122970511b8de75e59fb1ad0 7643 samtools_0.1.17-1.debian.tar.gz
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--
Processing of sequence alignments in SAM and BAM formats.
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