[med-svn] [SCM] samtools branch, meta, updated. meta/0.1.16-1-3-g3df22f3
Charles Plessy
plessy at debian.org
Tue Sep 6 08:39:14 UTC 2011
The following commit has been merged in the meta branch:
commit 3df22f30b17226c5078d7a7d3f738b442fd13b71
Author: Charles Plessy <plessy at debian.org>
Date: Tue Sep 6 17:33:33 2011 +0900
Built 0.1.18-1 on amd64 for upload.
diff --git a/amd64.changes b/amd64.changes
index 6d14215..7c269be 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -15,46 +15,45 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * 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)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 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
+ 5760c0f623d310931b826f819b29dcbe813c7767 1946 samtools_0.1.18-1.dsc
+ 77be35df7a90c288a003ff826ba99aef53b2fbe6 379306 samtools_0.1.18.orig.tar.bz2
+ 7dea5cc145e36f737dc8baf6badf1c328570da20 7593 samtools_0.1.18-1.debian.tar.gz
+ c68cd7d0107e349061c617d5b5b03e2d194d6055 528100 samtools_0.1.18-1_amd64.deb
+ 1d857175fa5cbfd2a4a2438d75b8cba972472e41 154072 libbam-dev_0.1.18-1_amd64.deb
Checksums-Sha256:
- 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
+ 73a20e1a56a565aef3e551f70f245a1d102c58e65bd0ff71251ea01b4ea88716 1946 samtools_0.1.18-1.dsc
+ f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16 379306 samtools_0.1.18.orig.tar.bz2
+ 307e711fc2c9f123f3fa60bf5935a17487e5b3b4b68192d2d98e54496494bde6 7593 samtools_0.1.18-1.debian.tar.gz
+ 58bdc966e27240dd40f3360217c61da6c1aec7a68de9ab5ad5142211c5d03a26 528100 samtools_0.1.18-1_amd64.deb
+ 8b93deaa8e3ca489689405598f1bbdfc209f57ae306e1d614468c3df74d906bd 154072 libbam-dev_0.1.18-1_amd64.deb
Files:
- 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
+ b4fe5f3fe42d1ac708150946ed4611d8 1946 science optional samtools_0.1.18-1.dsc
+ 71dab132e21c0766f0de84c2371a9157 379306 science optional samtools_0.1.18.orig.tar.bz2
+ c129651f68209b9cd88c84637fdba478 7593 science optional samtools_0.1.18-1.debian.tar.gz
+ 3ff72808597c8549d9646c92b27e761a 528100 science optional samtools_0.1.18-1_amd64.deb
+ 50297b7d71115ba69ba85ce8cac86497 154072 libdevel optional libbam-dev_0.1.18-1_amd64.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
-iQIcBAEBCAAGBQJOGugyAAoJEMW9bI8ildUCN4MP/iW0UKkNnhVSulAhb4V3KR3U
-34YdBfKs1EVZPOlN9HFlgMbJSb3afViRz5X9LVT7zIWPQOlhMK4f49qx7Al3Nc3l
-/V1eSu6NnmU1vGOoNsJ2H3tn2qdfpm50JPueoyV/07g8rTvIpuTY0pK6QD1q6Q3y
-vmAxT145Z7eIR+WNtkBZbptbALUAtfgkI20sSnu4vImK4SKScFOM6F7lc8KCLt/g
-2OAWyo7xyRnJxZpjvqM9aj4VQVU8ewU1p/7EfKZhxf1zwE6HIHvrCe534Eov0WOG
-+BN2JF11PhuwSXtdZpXXEEK7KA0b34TVPbxpq1T9qz70gZ5VQVbilkvW/eSPIR/X
-o5N71HRiw+07eOl0w+4+LsQThai05AgmMibMkWPnzJx5iJnMBjEsewff+aHi8Tu7
-c0fOOOAyCa3jwTd+4fTXCHFtoSoA+h5OEb3BuYgxTVZO0EYlCNpP/p/FvyJulnVF
-l2j4zFq4ggHJPOVQk/8C934XFfsUuOqxSg67kRwVzynyXfrr+knDJDgdSFM2/60c
-FpqzjGDfkActIaRHoIlJkKsPmg6HeTNG9sv3kkRws9dorWjDiZQo2sIQ6dorBH5G
-jEOHjr+MHGmsGxjB8NppuQ7LYMHJdiGXGhgjXb+FL6cAmD4Ps23PHpwPf5lrl4dV
-NWmoyBHK/MFRHFqROX3G
-=iadb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+=bNgQ
-----END PGP SIGNATURE-----
diff --git a/amd64.log b/amd64.log
index 7863cc8..0cd904e 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,18 +1,18 @@
-sbuild (Debian sbuild) 0.62.4 (25 Jun 2011) on anx191
+sbuild (Debian sbuild) 0.62.5 (13 Jul 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.17-1 (amd64) 11 Jul 2011 21:06 ║
+║ samtools 0.1.18-1 (amd64) 06 Sep 2011 17:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.17-1
-Source Version: 0.1.17-1
+Version: 0.1.18-1
+Source Version: 0.1.18-1
Distribution: unstable
Architecture: amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-eg6khG/samtools-0.1.18' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-eg6khG' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-9b3324e0-1f62-47c6-8efe-a3cd5862fbbd' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -35,14 +35,14 @@ Reading state information...
Local sources
─────────────
-samtools_0.1.17-1.dsc exists in .; copying to chroot
+samtools_0.1.18-1.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-OkL_5I/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-0YalQJ/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -58,7 +58,7 @@ 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'.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-5aucVI/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
@@ -87,25 +87,25 @@ The following NEW packages will be installed:
sbuild-build-depends-samtools-dummy zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/10.2 MB of archives.
+Need to get 0 B/10.1 MB of archives.
After this operation, 29.7 MB of additional disk space will be used.
Selecting previously deselected package libpipeline1.
-(Reading database ... 11027 files and directories currently installed.)
+(Reading database ... 11007 files and directories currently installed.)
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-3_amd64.deb) ...
+Selecting previously deselected package libpcre3.
+Unpacking libpcre3 (from .../libpcre3_8.12-4_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) ...
+Unpacking man-db (from .../man-db_2.6.0.2-2_amd64.deb) ...
Selecting previously deselected package libmagic1.
Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package file.
Unpacking file (from .../file_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package gettext-base.
-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) ...
+Unpacking gettext-base (from .../gettext-base_0.18.1.1-4_amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-3_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-4_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -115,15 +115,15 @@ Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
Selecting previously deselected package libunistring0.
Unpacking libunistring0 (from .../libunistring0_0.9.3-4_amd64.deb) ...
Selecting previously deselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
+Unpacking gettext (from .../gettext_0.18.1.1-4_amd64.deb) ...
Selecting previously deselected package intltool-debian.
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_8.9.0_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.9.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.94_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.96_all.deb) ...
Selecting previously deselected package diffstat.
Unpacking diffstat (from .../diffstat_1.54-1_amd64.deb) ...
Selecting previously deselected package libncurses5-dev.
@@ -135,24 +135,24 @@ 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 libpipeline1 (1.2.0-3) ...
+Setting up libpcre3 (8.12-4) ...
Setting up groff-base (1.21-6) ...
-Setting up man-db (2.6.0.2-1) ...
+Setting up man-db (2.6.0.2-2) ...
Building database of manual pages ...
Setting up libmagic1 (5.04-5+b1) ...
Setting up file (5.04-5+b1) ...
-Setting up gettext-base (0.18.1.1-3) ...
-Setting up libpcre3 (8.12-3) ...
-Setting up libxml2 (2.7.8.dfsg-3) ...
+Setting up gettext-base (0.18.1.1-4) ...
+Setting up libxml2 (2.7.8.dfsg-4) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.28.6-1) ...
No schema files found: doing nothing.
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-4) ...
-Setting up gettext (0.18.1.1-3) ...
+Setting up gettext (0.18.1.1-4) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu1) ...
-Setting up debhelper (8.9.0) ...
-Setting up cdbs (0.4.94) ...
+Setting up debhelper (8.9.6) ...
+Setting up cdbs (0.4.96) ...
Setting up diffstat (1.54-1) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up quilt (0.48-7) ...
@@ -164,8 +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_2.21.52.20110707-1 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
+Toolchain package versions: binutils_2.21.53.20110823-3 dpkg-dev_1.16.0.3 g++-4.6_4.6.1-9 gcc-4.6_4.6.1-9 libc6-dev_2.13-18 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 linux-libc-dev_3.0.0-3
+Package versions: apt_0.8.15.6 base-files_6.5 base-passwd_3.5.23 bash_4.1-3 binutils_2.21.53.20110823-3 bsdmainutils_8.2.3 bsdutils_1:2.19.1-5 build-essential_11.5 bzip2_1.0.5-7 cdbs_0.4.96 coreutils_8.5-1 cpp_4:4.6.1-2 cpp-4.6_4.6.1-9 dash_0.5.7-1 debconf_1.5.41 debconf-i18n_1.5.41 debfoster_2.7-1.1 debhelper_8.9.6 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_1.18-1 file_5.04-5+b1 findutils_4.4.2-1+b1 g++_4:4.6.1-2 g++-4.6_4.6.1-9 gcc_4:4.6.1-2 gcc-4.6_4.6.1-9 gcc-4.6-base_4.6.1-9 gettext_0.18.1.1-4 gettext-base_0.18.1.1-4 gnupg_1.4.11-3 gpgv_1.4.11-3 grep_2.9-2 groff-base_1.21-6 gzip_1.4-1 hostname_3.06 html2text_1.3.2a-15 initscripts_2.88dsf-13.11 insserv_1.14.0-2.1 intltool-debian_0.35.0+20060710.1 libacl1_2.2.51-3 libattr1_1:2.4.46-3 libblkid1_2.19.1-5 libbz2-1.0_1.0.5-7 libc-bin_2.13-18 libc-dev-bin_2.13-18 libc6_2.13-18 libc6-dev_2.13-18 libclass-isa-perl_0.36-2 libcloog-ppl0_0.15.9-3 libcomerr2_1.42~WIP-2011-07-02-1 libcroco3_0.6.2-1 libdb5.1_5.1.25-11 libdpkg-perl_1.16.0.3 libgc1c2_1:7.1-8 libgcc1_1:4.6.1-9 libgdbm3_1.8.3-10 libglib2.0-0_2.28.6-1 libgmp10_2:5.0.2+dfsg-1 libgmpxx4ldbl_2:5.0.2+dfsg-1 libgomp1_4.6.1-9 libgpm2_1.20.4-4 liblocale-gettext-perl_1.05-7 liblzma2_5.1.1alpha+20110809-2 libmagic1_5.04-5+b1 libmount1_2.19.1-5 libmpc2_0.9-3 libmpfr4_3.0.1-6 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_8.12-4 libpipeline1_1.2.0-3 libpng12-0_1.2.46-3 libpod-plainer-perl_1.03-1 libppl-c4_0.11.2-4 libppl9_0.11.2-4 libpwl5_0.11.2-4 libquadmath0_4.6.1-9 libreadline6_6.2-4 libselinux1_2.1.0-1 libsepol1_2.1.0-1.1 libslang2_2.2.4-3 libss2_1.42~WIP-2011-07-02-1 libstdc++6_4.6.1-9 libstdc++6-4.6-dev_4.6.1-9 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-4 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-4 libusb-0.1-4_2:0.1.12-19 libuuid1_2.19.1-5 libxml2_2.7.8.dfsg-4 linux-libc-dev_3.0.0-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-28 make_3.81-8.1 man-db_2.6.0.2-2 mawk_1.3.3-15 mount_2.19.1-5 multiarch-support_2.13-18 ncurses-base_5.9-1 ncurses-bin_5.9-1 passwd_1:4.1.4.2+svn3283-3 patch_2.6.1-2 perl_5.12.4-4 perl-base_5.12.4-4 perl-modules_5.12.4-4 po-debconf_1.0.16+nmu1 quilt_0.48-7 readline-common_6.2-4 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-13.11 sysvinit_2.88dsf-13.11 sysvinit-utils_2.88dsf-13.11 tar_1.26-2 tzdata_2011i-2 util-linux_2.19.1-5 xz-utils_5.1.1alpha+20110809-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -175,10 +175,10 @@ Package versions: apt_0.8.15.1 base-files_6.4 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-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: warning: extracting unsigned source package (samtools_0.1.18-1.dsc)
+dpkg-source: info: extracting samtools in samtools-0.1.18
+dpkg-source: info: unpacking samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.18-1.debian.tar.gz
dpkg-source: info: applying no-pileup-tests.patch
Check disc space
@@ -196,7 +196,7 @@ 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_SESSION_ID=sid-amd64-sbuild-9b3324e0-1f62-47c6-8efe-a3cd5862fbbd
SCHROOT_UID=31051
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -213,9 +213,9 @@ 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 0.1.17-1
+dpkg-buildpackage: source version 0.1.18-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.17
+ dpkg-source --before-build samtools-0.1.18
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
@@ -230,7 +230,7 @@ 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 `/«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
+rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim seqtk *~ *.a
make[2]: Leaving directory `/«PKGBUILDDIR»/misc'
make[1]: Leaving directory `/«PKGBUILDDIR»'
rm -f debian/stamp-makefile-check
@@ -249,13 +249,13 @@ 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-0.1.17
+ dpkg-source -b samtools-0.1.18
dpkg-source: info: using source format `3.0 (quilt)'
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
+dpkg-source: info: building samtools using existing ./samtools_0.1.18.orig.tar.bz2
+dpkg-source: info: building samtools in samtools_0.1.18-1.debian.tar.gz
+dpkg-source: info: building samtools in samtools_0.1.18-1.dsc
debian/rules build
test -x debian/rules
mkdir -p "."
@@ -310,7 +310,7 @@ gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D
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:175:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
+em.c:174:12: 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
@@ -367,8 +367,12 @@ gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o md5fa.o md5fa.c
gcc -g -O2 -g -O2 -Wall -fPIC -o md5fa md5.o md5fa.o -lz
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
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o wgsim.o wgsim.c
+gcc -g -O2 -g -O2 -Wall -fPIC -o wgsim wgsim.o -lm -lz
+gcc -g -O2 -g -O2 -Wall -fPIC -c -I.. -o seqtk.o seqtk.c
+seqtk.c: In function 'stk_comp':
+seqtk.c:143:16: warning: variable 'lc' set but not used [-Wunused-but-set-variable]
+gcc -g -O2 -g -O2 -Wall -fPIC -o seqtk seqtk.o -lm -lz
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
@@ -478,19 +482,19 @@ dh_shlibdeps -plibbam-dev
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_0.1.17-1_amd64.deb'.
+dh_builddeb -psamtools -- -Z=xz
+dpkg-deb: building package `samtools' in `../samtools_0.1.18-1_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_0.1.17-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.17-1_amd64.changes
+dh_builddeb -plibbam-dev -- -Z=xz
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.18-1_amd64.deb'.
+ dpkg-genchanges >../samtools_0.1.18-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.17
+ dpkg-source --after-build samtools-0.1.18
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110711-2107
+Build finished at 20110906-1721
Finished
────────
@@ -502,15 +506,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_amd64.changes:
+samtools_0.1.18-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Mon, 11 Jul 2011 21:04:30 +0900
+Date: Tue, 06 Sep 2011 16:52:04 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.17-1
+Version: 0.1.18-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -519,49 +523,48 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.17-1) unstable; urgency=low
+ samtools (0.1.18-1) unstable; urgency=low
.
- * 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)
+ [b990d9d3] New upstream release.
+ [d59366b9] Updated copyright statements.
+ [aa08abe5] Compress binary packages with xz.
+ [9a36c994] Added a DEP 3 header to debian/patches/no-pileup-tests.patch.
Checksums-Sha1:
- 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
+ 45e58ef06182228c5b837f4e6e6f2dd345ed539a 1060 samtools_0.1.18-1.dsc
+ 77be35df7a90c288a003ff826ba99aef53b2fbe6 379306 samtools_0.1.18.orig.tar.bz2
+ 7dea5cc145e36f737dc8baf6badf1c328570da20 7593 samtools_0.1.18-1.debian.tar.gz
+ c68cd7d0107e349061c617d5b5b03e2d194d6055 528100 samtools_0.1.18-1_amd64.deb
+ 1d857175fa5cbfd2a4a2438d75b8cba972472e41 154072 libbam-dev_0.1.18-1_amd64.deb
Checksums-Sha256:
- 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
+ be90f66077fc64c4800b13a95f27e2254a3737d7c5011403f76d1a9bb3bec484 1060 samtools_0.1.18-1.dsc
+ f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16 379306 samtools_0.1.18.orig.tar.bz2
+ 307e711fc2c9f123f3fa60bf5935a17487e5b3b4b68192d2d98e54496494bde6 7593 samtools_0.1.18-1.debian.tar.gz
+ 58bdc966e27240dd40f3360217c61da6c1aec7a68de9ab5ad5142211c5d03a26 528100 samtools_0.1.18-1_amd64.deb
+ 8b93deaa8e3ca489689405598f1bbdfc209f57ae306e1d614468c3df74d906bd 154072 libbam-dev_0.1.18-1_amd64.deb
Files:
- 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
+ 9e57a71fdfa8ee2942acb84456d347a1 1060 science optional samtools_0.1.18-1.dsc
+ 71dab132e21c0766f0de84c2371a9157 379306 science optional samtools_0.1.18.orig.tar.bz2
+ c129651f68209b9cd88c84637fdba478 7593 science optional samtools_0.1.18-1.debian.tar.gz
+ 3ff72808597c8549d9646c92b27e761a 528100 science optional samtools_0.1.18-1_amd64.deb
+ 50297b7d71115ba69ba85ce8cac86497 154072 libdevel optional libbam-dev_0.1.18-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.17-1_amd64.deb
+samtools_0.1.18-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 592564 bytes: control archive= 1761 bytes.
+ size 528100 bytes: control archive= 1760 bytes.
786 bytes, 16 lines control
2453 bytes, 37 lines md5sums
Package: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1068
+ Installed-Size: 1072
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -574,23 +577,23 @@ samtools_0.1.17-1_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 2011-07-11 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/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/samtools/
+-rwxr-xr-x root/root 11832 2011-09-06 17:21 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 17968 2011-09-06 17:21 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8688 2011-09-06 17:21 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 8080 2011-09-06 17:21 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 8144 2011-09-06 17:21 ./usr/lib/samtools/maq2sam-long
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/bin/
+-rwxr-xr-x root/root 363832 2011-09-06 17:21 ./usr/bin/samtools
+-rwxr-xr-x root/root 24488 2011-09-06 17:21 ./usr/bin/razip
+-rwxr-xr-x root/root 130528 2011-09-06 17:21 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./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 2011-07-11 21:07 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-09-06 17:21 ./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
@@ -602,43 +605,43 @@ drwxr-xr-x root/root 0 2011-07-11 21:07 ./usr/share/samtools/
-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 2011-07-11 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/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/man/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2011-09-06 17:21 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 9890 2011-09-06 17:21 ./usr/share/man/man1/samtools.1.gz
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./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 2011-07-11 21:07 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2011-09-06 17:21 ./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 9930 2011-07-07 11:59 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 10122 2011-09-03 01:58 ./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 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
+-rw-r--r-- root/root 5502 2011-09-06 16:01 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 1966 2011-09-06 17:21 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1676 2011-09-06 16:52 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 1031 2011-09-06 16:01 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 592 2011-09-06 16:01 ./usr/share/doc/samtools/reference
+lrwxrwxrwx root/root 0 2011-09-06 17:21 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.17-1_amd64.deb
+libbam-dev_0.1.18-1_amd64.deb
─────────────────────────────
new debian package, version 2.0.
- size 170236 bytes: control archive= 927 bytes.
+ size 154072 bytes: control archive= 924 bytes.
674 bytes, 15 lines control
715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.17-1
+ Version: 0.1.18-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 476
+ Installed-Size: 480
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -649,25 +652,25 @@ libbam-dev_0.1.17-1_amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-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/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/lib/
+-rw-r--r-- root/root 323274 2011-09-06 17:21 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/include/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./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 2011-07-07 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 24720 2011-09-03 01:58 ./usr/include/samtools/bam.h
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./usr/share/doc/
+drwxr-xr-x root/root 0 2011-09-06 17:21 ./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 9930 2011-07-07 11:59 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 10122 2011-09-03 01:58 ./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 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
+-rw-r--r-- root/root 5502 2011-09-06 16:01 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 1676 2011-09-06 16:52 ./usr/share/doc/libbam-dev/changelog.Debian.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -679,7 +682,6 @@ 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
@@ -716,7 +718,7 @@ The following packages will be REMOVED:
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, 29.7 MB disk space will be freed.
-(Reading database ... 12442 files and directories currently installed.)
+(Reading database ... 12421 files and directories currently installed.)
Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
Removing debhelper ...
@@ -756,18 +758,18 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12220
+Build-Space: 12700
Build-Time: 23
Distribution: unstable
Install-Time: 27
-Job: samtools_0.1.17-1.dsc
+Job: samtools_0.1.18-1.dsc
Lintian: pass
Package: samtools
-Package-Time: 53
-Source-Version: 0.1.17-1
-Space: 12220
+Package-Time: 51
+Source-Version: 0.1.18-1
+Space: 12700
Status: successful
-Version: 0.1.17-1
+Version: 0.1.18-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110711-2107
-Build needed 00:00:53, 12220k disc space
+Finished at 20110906-1721
+Build needed 00:00:51, 12700k disc space
diff --git a/dsc b/dsc
index f74ec89..010349e 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, libbam-dev
Architecture: any
-Version: 0.1.17-1
+Version: 0.1.18-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -15,29 +15,29 @@ 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, quilt, libncurses5-dev, zlib1g-dev
Checksums-Sha1:
- 4d2ef4273d9f71cd1f504f43c596970845d78718 373930 samtools_0.1.17.orig.tar.bz2
- 8b5a95897b302b2433141da51e23bd0a7bb10634 7643 samtools_0.1.17-1.debian.tar.gz
+ 77be35df7a90c288a003ff826ba99aef53b2fbe6 379306 samtools_0.1.18.orig.tar.bz2
+ 7dea5cc145e36f737dc8baf6badf1c328570da20 7593 samtools_0.1.18-1.debian.tar.gz
Checksums-Sha256:
- aeff504fc972d3357f05ab4ad76d9562dac5954d6f6fc90153f7d778d1a30a3e 373930 samtools_0.1.17.orig.tar.bz2
- d13d2d8257a52154c0159cad5efdc596657a3503cfc8bcc31f7649771019c9d8 7643 samtools_0.1.17-1.debian.tar.gz
+ f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16 379306 samtools_0.1.18.orig.tar.bz2
+ 307e711fc2c9f123f3fa60bf5935a17487e5b3b4b68192d2d98e54496494bde6 7593 samtools_0.1.18-1.debian.tar.gz
Files:
- 9549f7a6bba894766df9c3dd18d61f0b 373930 samtools_0.1.17.orig.tar.bz2
- 2167f175122970511b8de75e59fb1ad0 7643 samtools_0.1.17-1.debian.tar.gz
+ 71dab132e21c0766f0de84c2371a9157 379306 samtools_0.1.18.orig.tar.bz2
+ c129651f68209b9cd88c84637fdba478 7593 samtools_0.1.18-1.debian.tar.gz
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.10 (GNU/Linux)
-iQIcBAEBCAAGBQJOGugwAAoJEMW9bI8ildUCutAP/1SbigGHhQIiT1n7rjlnvXgo
-FHDn0Pdz0zi3lCh68bgHAOAQiEgdxQGY6EC39Mnp4qEeNKBLIgIZMwAl3OcqCCOl
-h3FBcDIbb/Km6YlF+Xwrhb1YkrIHgElVENVQRRwTC01VOKJiEq0liuRWkcaw7qp+
-EfzRAdbyVpi4YWkceh9i9czXvXiLWntiCUJZ4JPXIHS/gMaEtM58rXQ3UCdusx3N
-YOCKS+2er83TbqWflcCRSXvSSlDpYAM/c1qENLJh4clMCN7p1OK7UHcg6GvHs38n
-ug4UwCqoiilNFWDhLdkJOjWBxyS9IkXrh8aQdgdsYw9wyz4HyL2NYW7gHoXCQ2TO
-TERV19OEFEuu6MCf71EDTM3TL3Q47pgPr/xlCG8K1FQcw1U23dLPCwtYq1ftmHGK
-W0UIuo17MiWRFaRt0wBxPCxR7KPkIKEUMq5hbFmU+QYLKgKyu74Sh6Tn09M8Akic
-JilGpai2v43VvIsqP2ueE2M8osrKqbjN1IVvBJubGhD215emIty99I5X6/Toytbm
-3cMurtX29OArN4phZ6hFx5AIHyJ2mMWJHuelkidr2PXJ0r0HKdQOGFEFLLqS085W
-oLSFYKi7G+4ihHPyqsvVISU33eK8ChrnKbDnLsiaYzbH4Xzwk65ixMbPsaeR2+ir
-cs+8P6/rgrGwrPwMkHqI
-=PQer
+iQIcBAEBCAAGBQJOZdphAAoJEMW9bI8ildUC2gwP/2T38g+7FxGy7MrwVfI9iXZF
+Gng/HelT7eXmbrrLnsF/glSpI8tHFnAFerOn04VPBkd59K4fwDdGEqGKfaeD/piI
+UPxOGIDjDPux5WVbrwwVVmDQYsnMWiknbbUZengvAt5fHmMLNM4wnolAs+kax8+R
+qgObh0W/l6/iDhuQAG5ILC7di7KxXrfDEINSr3GQOPm9cq5Kukt6mvfNSwu3mj9R
+00yia/s02LhpdhRctFz+OSOE+xrCBNsXaLSYbWMCRlNwtF3f3LzU7PaxQodLWKfp
+6phLIzB8WBDT3QIpaZ8toGa5w+3hOP6+iOZcQQ997YfdJkdI9flma1wDLIT86kby
+cjbxkBZo0ZcF1Jkk54CZ3lcbMphcX0L3lXnGYqzsk2IGpTczJwNy+J7wWQKv5TG7
+O4KtSDdzSm0SHKKVz2oAjQh9wgJLicIpwcMg0b7uVUvdOvoTNcdRI2NNKH1Zw928
+AMMcNTJdJ40neFe+CIMNpEMoZQFZMeHOGD74997gH3XIYj7JHP7NmwG/a6+zeCD5
+r1B9rBO7aMFM6KQvmRLFsPURcj3bw9wVi84hRkQvkL+wgSVmQqS0N9IjkDRVMhMr
+bG2v4p7DWOLy+sqCfs3cH9DbljCZ6vmL3J3U/Jy3tHs9tVoByvpOvYjnWgbWnzTd
+NTiAYVLv7E3tj52TOG5I
+=JtXf
-----END PGP SIGNATURE-----
--
Processing of sequence alignments in SAM and BAM formats.
More information about the debian-med-commit
mailing list