[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. meta/0.1.14-1-3-g91cddec
Charles Plessy
plessy at debian.org
Thu May 19 04:42:34 UTC 2011
The following commit has been merged in the meta branch:
commit 91cddec85a1163993c8ccbb3d461054713acd4bc
Author: Charles Plessy <plessy at debian.org>
Date: Thu May 19 13:38:37 2011 +0900
Uploaded samtools_0.1.16-1_amd64.changes.
diff --git a/amd64.changes b/amd64.changes
index c4d4c1c..d5ffd53 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -14,46 +14,46 @@ 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 (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
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- bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
- 4f5a23bdbaa730c3c5e11e4e5792a00c9c0e5d3b 599104 samtools_0.1.15-1_amd64.deb
- 473799f45bf22dde0d9d89b1a84a3529d1c85840 169002 libbam-dev_0.1.15-1_amd64.deb
+ 42c68b748cd4379a7cf733829f96e72b5bf93fa4 1939 samtools_0.1.16-1.dsc
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+ dae61375b51af04266dbf80de13f9b9e0ccacb46 171096 libbam-dev_0.1.16-1_amd64.deb
Checksums-Sha256:
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+ c3e304bfd7c931cf256cc34556892b3edfd7a60dea78123b868f0dd8ab613130 1939 samtools_0.1.16-1.dsc
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+ f25fb6eba596d2dbd706afb60e286dabb0a047092ae4d592f764e30160d0da28 171096 libbam-dev_0.1.16-1_amd64.deb
Files:
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- caf1cac191fdabd57a309e36f359c047 374429 science optional samtools_0.1.15.orig.tar.bz2
- 8f3586257c58ea4371d4e83ebcb7a74e 7005 science optional samtools_0.1.15-1.debian.tar.gz
- f11a7ccf86ab2a9b39be07d1191e3586 599104 science optional samtools_0.1.15-1_amd64.deb
- 302c9810d2f9384ab504313a66e8beb8 169002 libdevel optional libbam-dev_0.1.15-1_amd64.deb
+ 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
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diff --git a/amd64.log b/amd64.log
index 39f2570..69e851c 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,24 +1,26 @@
sbuild (Debian sbuild) 0.62.2 (05 Apr 2011) on anx191
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.15-1 (amd64) 12 Apr 2011 19:54 ║
+║ samtools 0.1.16-1 (amd64) 19 mai 2011 13:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.15-1
-Source Version: 0.1.15-1
+Version: 0.1.16-1
+Source Version: 0.1.16-1
Distribution: unstable
Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/samtools-uPEbZJ' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-874fd008-a454-4a94-ad87-a3cabe614343' with '«CHROOT»'
+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»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
+Hit http://ftp.jp.debian.org sid InRelease
+Hit http://ftp.jp.debian.org sid/main amd64 Packages/DiffIndex
+Hit http://ftp.jp.debian.org sid/main TranslationIndex
Hit http://ftp.riken.jp sid InRelease
-Hit http://ftp.riken.jp sid/main Sources/DiffIndex
Hit http://ftp.riken.jp sid/main amd64 Packages/DiffIndex
Hit http://ftp.riken.jp sid/main TranslationIndex
Reading package lists...
@@ -35,14 +37,14 @@ Reading state information...
Local sources
─────────────
-samtools_0.1.15-1.dsc exists in .; copying to chroot
+samtools_0.1.16-1.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-RyGduq/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-EDTXTU/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
@@ -61,12 +63,12 @@ debconf: delaying package configuration, since apt-utils is not installed
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 ... 10291 files and directories currently installed.)
+(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-uzfR0a/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-gHdSaO/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Reading package lists...
@@ -83,8 +85,8 @@ The following extra packages will be installed:
intltool-debian libcroco3 libglib2.0-0 libmagic1 libncurses5-dev libpcre3
libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation devscripts doc-base dh-make gettext-doc
- groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
+ ncurses-doc less www-browser libmail-box-perl
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl
@@ -95,35 +97,35 @@ 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, 21 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/11.2 MB of archives.
-After this operation, 31.3 MB of additional disk space will be used.
+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 ... 10291 files and directories currently installed.)
+(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) ...
Selecting previously deselected package libpipeline1.
Unpacking libpipeline1 (from .../libpipeline1_1.2.0-1_amd64.deb) ...
Selecting previously deselected package man-db.
-Unpacking man-db (from .../man-db_2.6.0.1-1_amd64.deb) ...
+Unpacking man-db (from .../man-db_2.6.0.2-1_amd64.deb) ...
Selecting previously deselected package libmagic1.
-Unpacking libmagic1 (from .../libmagic1_5.04-5_amd64.deb) ...
+Unpacking libmagic1 (from .../libmagic1_5.04-5+b1_amd64.deb) ...
Selecting previously deselected package file.
-Unpacking file (from .../archives/file_5.04-5_amd64.deb) ...
+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) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-2+b1_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
-Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.4-1_amd64.deb) ...
+Unpacking libglib2.0-0 (from .../libglib2.0-0_2.28.6-1_amd64.deb) ...
Selecting previously deselected package libcroco3.
Unpacking libcroco3 (from .../libcroco3_0.6.2-1_amd64.deb) ...
Selecting previously deselected package libunistring0.
-Unpacking libunistring0 (from .../libunistring0_0.9.3-3_amd64.deb) ...
+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) ...
Selecting previously deselected package intltool-debian.
@@ -131,9 +133,9 @@ 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_8.1.3_all.deb) ...
+Unpacking debhelper (from .../debhelper_8.1.6_all.deb) ...
Selecting previously deselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.92_all.deb) ...
+Unpacking cdbs (from .../archives/cdbs_0.4.93_all.deb) ...
Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-1_amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
@@ -145,23 +147,23 @@ update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write)
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 man-db (2.6.0.1-1) ...
+Setting up man-db (2.6.0.2-1) ...
Building database of manual pages ...
-Setting up libmagic1 (5.04-5) ...
-Setting up file (5.04-5) ...
+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) ...
+Setting up libxml2 (2.7.8.dfsg-2+b1) ...
Setting up html2text (1.3.2a-15) ...
-Setting up libglib2.0-0 (2.28.4-1) ...
+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 (0.9.3-3) ...
+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 (8.1.3) ...
-Setting up cdbs (0.4.92) ...
+Setting up debhelper (8.1.6) ...
+Setting up cdbs (0.4.93) ...
Setting up libncurses5-dev (5.9-1) ...
Setting up zlib1g-dev (1:1.2.3.4.dfsg-3) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
@@ -171,8 +173,8 @@ Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 2.6.32-5-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.21.0.20110327-3 dpkg-dev_1.16.0.1 g++-4.5_4.5.2-8 gcc-4.5_4.5.2-8 libc6-dev_2.11.2-13 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 linux-libc-dev_2.6.38-3
-Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binutils_2.21.0.20110327-3 bsdmainutils_8.2.2 bsdutils_1:2.17.2-9.1 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.92 coreutils_8.5-1 cpp_4:4.5.2-5 cpp-4.5_4.5.2-8 dash_0.5.5.1-7.4 debconf_1.5.38 debconf-i18n_1.5.38 debfoster_2.7-1.1 debhelper_8.1.3 debian-archive-keyring_2010.08.28 debianutils_3.4.4 diffutils_1:3.0-1 dpkg_1.16.0.1 dpkg-dev_1.16.0.1 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.15.1-1 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.5.2-5 g++-4.5_4.5.2-8 gcc_4:4.5.2-5 gcc-4.4-base_4.4.5-15 gcc-4.5_4.5.2-8 gcc-4.5-base_4.5.2-8 gcc-4.6-base_4.6.0-2 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-13.1 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_2.11.2-13 libc-dev-bin_2.11.2-13 libc6_2.11.2-13 libc6-dev_2.11.2-13 libcloog-ppl0_0.15.9-3 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-12 libdb4.8_4.8.30-5 libdpkg-perl_1.16.0.1 libelfg0_0.8.13-1 libgc1c2_1:7.1-7 libgcc1_1:4.6.0-2 libgdbm3_1.8.3-9 libglib2.0-0_2.28.4-1 libgmp10_2:5.0.1+dfsg-7 libgmpxx4ldbl_2:5.0.1+dfsg-7 libgomp1_4.6.0-2 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpc2_0.9-2 libmpfr4_3.0.0-9 libncurses5_5.9-1 libncurses5-dev_5.9-1 libpam-modules_1.1.2-2 libpam-runtime_1.1.2-2 libpam0g_1.1.2-2 libpcre3_8.12-3 libpipeline1_1.2.0-1 libppl-c4_0.11.2-3 libppl9_0.11.2-3 libpwl5_0.11.2-3 libreadline6_6.1-3 libselinux1_2.0.98-1 libsepol1_2.0.42-1 libslang2_2.2.3-3 libss2_1.41.12-2 libstdc++6_4.6.0-2 libstdc++6-4.5-dev_4.5.2-8 libtext-charwidth-perl_0.04-6 libtext-iconv-perl_1.7-2 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libunistring0_0.9.3-3 libusb-0.1-4_2:0.1.12-17 libuuid1_2.17.2-9.1 libxml2_2.7.8.dfsg-2 linux-libc-dev_2.6.38-3 login_1:4.1.4.2+svn3283-3 lsb-base_3.2-27 make_3.81-8.1 man-db_2.6.0.1-1 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_5.10.1-19 perl-base_5.10.1-19 perl-modules_5.10.1-19 po-debconf_1.0.16+nmu1 readline-common_6.1-3 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-13.1 sysvinit_2.88dsf-13.1 sysvinit-utils_2.88dsf-13.1 tar_1.25-3 tzdata_2011e-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_2.21.51.20110421-5 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -182,13 +184,10 @@ Package versions: apt_0.8.13.2 base-files_6.3 base-passwd_3.5.22 bash_4.1-3 binu
Unpack source
─────────────
-gpgv: keyblock resource `/var/lib/sbuild/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Apr 12 10:53:14 2011 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.15-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.15
-dpkg-source: info: unpacking samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.15-1.debian.tar.gz
+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
Check disc space
────────────────
@@ -204,132 +203,145 @@ 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 0.1.15-1
+dpkg-buildpackage: source version 0.1.16-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.15
+ dpkg-source --before-build samtools-0.1.16
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 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
+/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'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/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-0.1.15/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/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-0.1.15/misc'
-make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/misc'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
rm -f debian/stamp-makefile-check
dh_clean
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-0.1.15
+ dpkg-source -b samtools-0.1.16
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_0.1.15.orig.tar.bz2
-dpkg-source: info: building samtools in samtools_0.1.15-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.15-1.dsc
+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
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 -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -g -O2 -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 -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 -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 -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 -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 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
+/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'
+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]
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.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_aux.c -o bam_aux.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.c -o bam.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_import.c -o bam_import.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.c -o sam.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_index.c -o bam_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. bam_pileup.c -o bam_pileup.o
+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
+gcc -c -g -O2 -g -O2 -Wall -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.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_sort.c -o bam_sort.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_header.c -o sam_header.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_reheader.c -o bam_reheader.o
+bam_reheader.c: In function 'bam_reheader':
+bam_reheader.c:11:16: warning: variable 'old' 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. kprobaln.c -o kprobaln.o
+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-0.1.15'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
-gcc -c -g -O2 -g -O2 -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 -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 -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 -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 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. ld.c -o ld.o
-gcc -c -g -O2 -g -O2 -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 -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 -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 -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 ld.o kfunc.o index.o fet.o bcf2qcall.o
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
+make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.16/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]
+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. 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'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
-gcc -c -g -O2 -g -O2 -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 -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 -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 -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 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -g -O2 -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 -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 -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-0.1.15'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15'
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/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
+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_rmdupse.c -o bam_rmdupse.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_mate.c -o bam_mate.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_stat.c -o bam_stat.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_color.c -o bam_color.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. bamtk.c -o bamtk.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. kaln.c -o kaln.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. bam2bcf.c -o bam2bcf.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. bam2bcf_indel.c -o bam2bcf_indel.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. errmod.c -o errmod.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. sample.c -o sample.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. cut_target.c -o cut_target.o
+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'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
+make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
+make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
-make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
+make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/bcftools'
+make[3]: Entering directory `/«BUILDDIR»/samtools-0.1.16/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
-gcc -g -O2 -g -O2 -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-0.1.15'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/bcftools'
-gcc -c -g -O2 -g -O2 -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 -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 -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-0.1.15/bcftools'
-make[2]: Entering directory `/«BUILDDIR»/samtools-0.1.15/misc'
-gcc -c -g -O2 -g -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -g -O2 -fPIC -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -g -O2 -fPIC -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -g -O2 -fPIC -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -g -O2 -fPIC -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -g -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -c -g -O2 -g -O2 -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 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.15/misc'
-gcc -c -g -O2 -g -O2 -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 -fPIC -o razip razf.o razip.o knetfile.o -lz
+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'
+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'
+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
+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
+make[2]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/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-0.1.15'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16'
touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -g -O2 -fPIC" CXXFLAGS="-g -O2 -g -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/«BUILDDIR»/samtools-0.1.15/examples'
+/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'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -358,7 +370,7 @@ 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-0.1.15/examples'
+make[1]: Leaving directory `/«BUILDDIR»/samtools-0.1.16/examples'
touch debian/stamp-makefile-check
fakeroot debian/rules binary
test -x debian/rules
@@ -385,6 +397,7 @@ 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
@@ -392,7 +405,7 @@ dh_bugfiles -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /«BUILDDIR»/samtools-0.1.15/debian/samtools/usr/share/doc/samtools/README.bcftools
+install -m 644 bcftools/README /«BUILDDIR»/samtools-0.1.16/debian/samtools/usr/share/doc/samtools/README.bcftools
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -406,6 +419,7 @@ 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
@@ -417,7 +431,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«BUILDDIR»/samtools-0.1.15/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /«BUILDDIR»/samtools-0.1.16/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -432,18 +446,18 @@ 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_0.1.15-1_amd64.deb'.
+dpkg-deb: building package `samtools' in `../samtools_0.1.16-1_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_0.1.15-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.15-1_amd64.changes
+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-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.15
+ dpkg-source --after-build samtools-0.1.16
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20110412-1955
+Build finished at 20110519-1325
Finished
────────
@@ -455,15 +469,15 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_amd64.changes:
+samtools_0.1.16-1_amd64.changes:
────────────────────────────────
Format: 1.8
-Date: Tue, 12 Apr 2011 19:44:41 +0900
+Date: Thu, 19 May 2011 13:24:25 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: source amd64
-Version: 0.1.15-1
+Version: 0.1.16-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -471,49 +485,49 @@ 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 (0.1.15-1) unstable; urgency=low
+ samtools (0.1.16-1) unstable; urgency=low
.
- * New upstream release.
- * Incremented Standards-Version to reflect conformance with Policy 3.9.2
- (debian/control, no changes needed).
- * debian/watch directly interrogates and downloads froms SourceForge.
+ * New upstream release, implementing SAM Spec v1.4.
+ * Distribute sam.h and the other headers in /usr/include/samtools.
+ Closes: #625622, #626044, LP: #690997.
Checksums-Sha1:
- 20f6292bd8be9f1b76132e75ef3d5a2455001a8d 1053 samtools_0.1.15-1.dsc
- 0a0f05928ba40ce95d4feda0cd0742ccd1b69e76 374429 samtools_0.1.15.orig.tar.bz2
- bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
- 4f5a23bdbaa730c3c5e11e4e5792a00c9c0e5d3b 599104 samtools_0.1.15-1_amd64.deb
- 473799f45bf22dde0d9d89b1a84a3529d1c85840 169002 libbam-dev_0.1.15-1_amd64.deb
+ 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
Checksums-Sha256:
- d53980cf064401993dd0f0c63207d3b4d0a81780f9d0dd8d7d6fba1c9e850162 1053 samtools_0.1.15-1.dsc
- 59cdd41c9697b5a2c8c57f1867266f8262058d280460d22cdd74606aa7d7047f 374429 samtools_0.1.15.orig.tar.bz2
- f7f94edc5b59dd11e1dee11346cc11f25b15dae8869074d840b89535ea1a2b53 7005 samtools_0.1.15-1.debian.tar.gz
- 5ab78897e9238eef643f4334cfc4cafd42531763fc97e619242cdbdcf5e42d3f 599104 samtools_0.1.15-1_amd64.deb
- 303f88901a79909ed1b5bcefb3ccdd99b0c39e4a0f8fdf5b6d2010dff585a443 169002 libbam-dev_0.1.15-1_amd64.deb
+ 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
Files:
- fd5e8017924e6f29a496bcdf9a6612de 1053 science optional samtools_0.1.15-1.dsc
- caf1cac191fdabd57a309e36f359c047 374429 science optional samtools_0.1.15.orig.tar.bz2
- 8f3586257c58ea4371d4e83ebcb7a74e 7005 science optional samtools_0.1.15-1.debian.tar.gz
- f11a7ccf86ab2a9b39be07d1191e3586 599104 science optional samtools_0.1.15-1_amd64.deb
- 302c9810d2f9384ab504313a66e8beb8 169002 libdevel optional libbam-dev_0.1.15-1_amd64.deb
+ 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
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.15-1_amd64.deb
+samtools_0.1.16-1_amd64.deb
───────────────────────────
new debian package, version 2.0.
- size 599104 bytes: control archive= 1787 bytes.
+ size 602354 bytes: control archive= 1788 bytes.
786 bytes, 16 lines control
2520 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1088
+ Installed-Size: 1092
Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -526,23 +540,23 @@ samtools_0.1.15-1_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 2011-04-12 19:55 ./
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/samtools/
--rwxr-xr-x root/root 11880 2011-04-12 19:55 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 19248 2011-04-12 19:55 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8560 2011-04-12 19:55 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 8128 2011-04-12 19:55 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 8224 2011-04-12 19:55 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/bin/
--rwxr-xr-x root/root 384272 2011-04-12 19:55 ./usr/bin/samtools
--rwxr-xr-x root/root 24768 2011-04-12 19:55 ./usr/bin/razip
--rwxr-xr-x root/root 114088 2011-04-12 19:55 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/samtools/
+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/
-rwxr-xr-x root/root 18572 2011-03-22 12:09 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2011-04-12 19:55 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2011-05-19 13:25 ./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
@@ -554,43 +568,43 @@ drwxr-xr-x root/root 0 2011-04-12 19:55 ./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 2011-04-12 19:55 ./usr/share/man/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/man/man1/
--rw-r--r-- root/root 2005 2011-04-12 19:55 ./usr/share/man/man1/bcftools.1.gz
--rw-r--r-- root/root 430 2011-04-12 19:55 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 8393 2011-04-12 19:55 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/samtools/examples/
+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/
-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 764 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2011-04-12 19:55 ./usr/share/doc/samtools/examples/ex1.bam.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 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 9003 2011-04-11 07:33 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 9373 2011-04-22 12:16 ./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 5287 2011-04-12 19:43 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1966 2011-04-12 19:55 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1362 2011-04-12 19:45 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 1031 2011-04-12 19:33 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2011-04-12 19:33 ./usr/share/doc/samtools/reference
+-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
-libbam-dev_0.1.15-1_amd64.deb
+libbam-dev_0.1.16-1_amd64.deb
─────────────────────────────
new debian package, version 2.0.
- size 169002 bytes: control archive= 900 bytes.
+ size 171096 bytes: control archive= 928 bytes.
674 bytes, 15 lines control
- 618 bytes, 10 lines md5sums
+ 715 bytes, 11 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.15-1
+ Version: 0.1.16-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 472
+ Installed-Size: 484
Section: libdevel
Priority: optional
Homepage: http://samtools.sourceforge.net
@@ -601,23 +615,25 @@ libbam-dev_0.1.15-1_amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/lib/
--rw-r--r-- root/root 323908 2011-04-12 19:55 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/include/
--rw-r--r-- root/root 17815 2011-03-02 04:50 ./usr/include/khash.h
--rw-r--r-- root/root 3188 2010-11-17 13:16 ./usr/include/faidx.h
--rw-r--r-- root/root 4617 2011-04-11 07:33 ./usr/include/bgzf.h
--rw-r--r-- root/root 24338 2011-04-11 07:33 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/
-drwxr-xr-x root/root 0 2011-04-12 19:55 ./usr/share/doc/libbam-dev/
+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/
+-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 33578 2011-03-02 04:50 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 9003 2011-04-11 07:33 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 9373 2011-04-22 12:16 ./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 5287 2011-04-12 19:43 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 1362 2011-04-12 19:45 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+-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
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -644,8 +660,8 @@ The following packages will be REMOVED:
po-debconf* sbuild-build-depends-core-dummy*
sbuild-build-depends-samtools-dummy* zlib1g-dev*
0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded.
-After this operation, 31.3 MB disk space will be freed.
-(Reading database ... 11732 files and directories currently installed.)
+After this operation, 29.5 MB disk space will be freed.
+(Reading database ... 12221 files and directories currently installed.)
Removing sbuild-build-depends-samtools-dummy ...
Removing cdbs ...
Removing debhelper ...
@@ -685,17 +701,17 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 12208
-Build-Time: 21
+Build-Space: 12588
+Build-Time: 23
Distribution: unstable
-Install-Time: 28
-Job: samtools_0.1.15-1.dsc
+Install-Time: 26
+Job: samtools_0.1.16-1.dsc
Package: samtools
-Package-Time: 51
-Source-Version: 0.1.15-1
-Space: 12208
+Package-Time: 56
+Source-Version: 0.1.16-1
+Space: 12588
Status: successful
-Version: 0.1.15-1
+Version: 0.1.16-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20110412-1955
-Build needed 00:00:51, 12208k disc space
+Finished at 20110519-1325
+Build needed 00:00:56, 12588k disc space
diff --git a/dsc b/dsc
index 0814b66..dc55d23 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, libbam-dev
Architecture: any
-Version: 0.1.15-1
+Version: 0.1.16-1
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, libncurses5-dev, zlib1g-dev
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- bc8b3ec45fc1bd706858596b68661a654678b46e 7005 samtools_0.1.15-1.debian.tar.gz
+ 4f00dad58f707efb84a4d0144b6245e4da4077e5 379809 samtools_0.1.16.orig.tar.bz2
+ abed22d9f1f442efa09bddb45ad442aa3f1d6e91 7161 samtools_0.1.16-1.debian.tar.gz
Checksums-Sha256:
- 59cdd41c9697b5a2c8c57f1867266f8262058d280460d22cdd74606aa7d7047f 374429 samtools_0.1.15.orig.tar.bz2
- f7f94edc5b59dd11e1dee11346cc11f25b15dae8869074d840b89535ea1a2b53 7005 samtools_0.1.15-1.debian.tar.gz
+ ae37c49f2414d1fabe597f68f2351f6cce4b6c0a1a512a5d739bbf759f80a726 379809 samtools_0.1.16.orig.tar.bz2
+ ccdae2d562a2cb58e2b68e37dc1cbc7aca49f9d79415cf51fabc7a7b1d37af9f 7161 samtools_0.1.16-1.debian.tar.gz
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- 8f3586257c58ea4371d4e83ebcb7a74e 7005 samtools_0.1.15-1.debian.tar.gz
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+ 1a535f5525a4a813346b611b1f9d8b19 7161 samtools_0.1.16-1.debian.tar.gz
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--
Processing of sequence alignments in SAM and BAM formats.
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