[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. 1123e8696adc2f17a212c73ceeb675a54a3e35ba
Charles Plessy
plessy at debian.org
Tue Dec 7 04:28:33 UTC 2010
The following commit has been merged in the meta branch:
commit 1123e8696adc2f17a212c73ceeb675a54a3e35ba
Author: Charles Plessy <plessy at debian.org>
Date: Tue Dec 7 13:29:31 2010 +0900
# Collected build log for mips.
diff --git a/mips.build b/mips.build
index 59b73d0..946901a 100644
--- a/mips.build
+++ b/mips.build
@@ -1,17 +1,17 @@
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN">
-<html><head><title>buildd.debian.org: log of samtools_0.1.10-1/mips received Thu Nov 18 08:46:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
-<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1">0.1.10-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.10-1;arch=mips">mips</a> >> Thu Nov 18 08:46:05 2010<pre>
+<html><head><title>buildd.debian.org: log of samtools_0.1.12a-1/mips received Sat Dec 4 07:50:05 2010</title><link rel="stylesheet" type="text/css" href="pkg.css"></head>
+<body><a href="build.cgi">Search</a> >> <a href="pkg.cgi?pkg=samtools">samtools</a> (<a href="http://bugs.debian.org/src:samtools">Bugs</a>/<a href="http://packages.qa.debian.org/samtools">PTS</a>/<a href="http://packages.debian.org/samtools">Packages</a>) >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1">0.1.12a-1</a> >> <a href="build.cgi?pkg=samtools;ver=0.1.12a-1;arch=mips">mips</a> >> Sat Dec 4 07:50:05 2010<pre>
sbuild (Debian sbuild) 0.60.0 (23 Feb 2010) on ball.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (mips) 18 Nov 2010 08:38 ║
+║ samtools 0.1.12a-1 (mips) 04 Dec 2010 07:42 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
+Version: 0.1.12a-1
Architecture: mips
-Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-b522fcbb-8ede-4893-98db-96e883e922ef/build/buildd-samtools_0.1.10-1-mips-Tg8JD2
-Start Time: 20101118-0838
+Chroot Build Dir: /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
+Start Time: 20101204-0742
Get:1 http://debian.netcologne.de unstable Release.gpg [835B]
Ign http://debian.netcologne.de/debian/ unstable/contrib Translation-en
Ign http://debian.netcologne.de/debian/ unstable/main Translation-en
@@ -22,20 +22,20 @@ Ign http://incoming.debian.org/debian/ unstable/main Translation-en
Get:4 http://incoming.debian.org Release.gpg [835B]
Ign http://incoming.debian.org/buildd-unstable/ Translation-en
Get:5 http://incoming.debian.org unstable Release [104kB]
-Get:6 http://debian.netcologne.de unstable/main Sources [4056kB]
+Get:6 http://debian.netcologne.de unstable/main Sources [4073kB]
Get:7 http://incoming.debian.org Release [1604B]
-Get:8 http://incoming.debian.org unstable/main Sources [4057kB]
-Get:9 http://debian.netcologne.de unstable/contrib Sources [39.0kB]
-Get:10 http://debian.netcologne.de unstable/non-free Sources [83.1kB]
-Get:11 http://debian.netcologne.de unstable/main mips Packages [6725kB]
+Get:8 http://incoming.debian.org unstable/main Sources [4071kB]
+Get:9 http://debian.netcologne.de unstable/contrib Sources [38.7kB]
+Get:10 http://debian.netcologne.de unstable/non-free Sources [83.8kB]
+Get:11 http://debian.netcologne.de unstable/main mips Packages [6730kB]
Get:12 http://debian.netcologne.de unstable/contrib mips Packages [51.5kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [38.9kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [83.2kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6724kB]
+Get:13 http://incoming.debian.org unstable/contrib Sources [38.7kB]
+Get:14 http://incoming.debian.org unstable/non-free Sources [83.8kB]
+Get:15 http://incoming.debian.org unstable/main mips Packages [6731kB]
Get:16 http://incoming.debian.org unstable/contrib mips Packages [51.5kB]
-Get:17 http://incoming.debian.org Sources [14.4kB]
-Get:18 http://incoming.debian.org Packages [249kB]
-Fetched 22.4MB in 49s (453kB/s)
+Get:17 http://incoming.debian.org Sources [10.0kB]
+Get:18 http://incoming.debian.org Packages [110kB]
+Fetched 22.3MB in 46s (478kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -55,18 +55,18 @@ Reading package lists...
Building dependency tree...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/samtools.git
-Need to get 361kB of source archives.
-Get:1 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (dsc) [1939B]
-Get:2 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (tar) [353kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.10-1 (diff) [6332B]
-Fetched 361kB in 0s (1826kB/s)
+Need to get 364kB of source archives.
+Get:1 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (dsc) [1946B]
+Get:2 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (tar) [356kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main samtools 0.1.12a-1 (diff) [6337B]
+Fetched 364kB in 0s (1758kB/s)
Download complete and in download only mode
Check arch
──────────
** Using build dependencies supplied by package:
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install build dependencies (internal resolver) │
@@ -98,12 +98,12 @@ The following NEW packages will be installed:
libunistring0 libxml2 man-db po-debconf zlib1g-dev
The following packages will be upgraded:
libncurses5 ncurses-bin
-2 upgraded, 19 newly installed, 0 to remove and 50 not upgraded.
+2 upgraded, 19 newly installed, 0 to remove and 54 not upgraded.
Need to get 12.3MB of archives.
After this operation, 37.2MB of additional disk space will be used.
Get:1 http://debian.netcologne.de/debian/ unstable/main ncurses-bin mips 5.7+20100313-4 [317kB]
Get:2 http://debian.netcologne.de/debian/ unstable/main libncurses5 mips 5.7+20100313-4 [349kB]
-Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.0.16 [208kB]
+Get:3 http://debian.netcologne.de/debian/ unstable/main bsdmainutils mips 8.0.17 [208kB]
Get:4 http://debian.netcologne.de/debian/ unstable/main groff-base mips 1.20.1-10 [1190kB]
Get:5 http://debian.netcologne.de/debian/ unstable/main man-db mips 2.5.7-6 [1251kB]
Get:6 http://debian.netcologne.de/debian/ unstable/main libmagic1 mips 5.04-5 [239kB]
@@ -123,7 +123,7 @@ Get:19 http://debian.netcologne.de/debian/ unstable/main cdbs all 0.4.89 [1240kB
Get:20 http://debian.netcologne.de/debian/ unstable/main libncurses5-dev mips 5.7+20100313-4 [1643kB]
Get:21 http://debian.netcologne.de/debian/ unstable/main zlib1g-dev mips 1:1.2.3.4.dfsg-3 [191kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.3MB in 2s (4993kB/s)
+Fetched 12.3MB in 2s (4710kB/s)
(Reading database ... 10123 files and directories currently installed.)
Preparing to replace ncurses-bin 5.7+20100313-3 (using .../ncurses-bin_5.7+20100313-4_mips.deb) ...
Unpacking replacement ncurses-bin ...
@@ -134,7 +134,7 @@ Unpacking replacement libncurses5 ...
Setting up libncurses5 (5.7+20100313-4) ...
Selecting previously deselected package bsdmainutils.
(Reading database ... 10123 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.16_mips.deb) ...
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_mips.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_mips.deb) ...
Selecting previously deselected package man-db.
@@ -171,7 +171,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_mips.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_mips.deb) ...
-Setting up bsdmainutils (8.0.16) ...
+Setting up bsdmainutils (8.0.17) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode.
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode.
Setting up groff-base (1.20.1-10) ...
@@ -197,7 +197,7 @@ Removing negative dependencies:
Checking correctness of source dependencies...
Kernel: Linux 2.6.32.2-dsa-mips-swarm mips (mips64)
Toolchain package versions: libc6-dev_2.11.2-6 dpkg-dev_1.15.8.5 linux-libc-dev_2.6.32-23 gcc-4.4_4.4.4-15 g++-4.4_4.4.4-15 binutils_2.20.1-15 libstdc++6-4.4-dev_4.4.4-15 libstdc++6_4.4.4-15
-Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.16 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 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_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Package versions: apt_0.8.5 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.2 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.4-2 cpp-4.4_4.4.4-15 dash_0.5.5.1-7 debconf_1.5.35 debconf-i18n_1.5.35 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.1 diffutils_1:3.0-1 dpkg_1.15.8.5 dpkg-dev_1.15.8.5 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-1 file_5.04-5 findutils_4.4.2-1 g++_4:4.4.4-2 g++-4.4_4.4.4-15 gcc_4:4.4.4-2 gcc-4.4_4.4.4-15 gcc-4.4-base_4.4.4-15 gettext_0.18.1.1-3 gettext-base_0.18.1.1-3 gnupg_1.4.10-4 gpgv_1.4.10-4 grep_2.6.3-3 groff-base_1.20.1-10 gzip_1.3.12-9 hostname_3.04 html2text_1.3.2a-15 initscripts_2.88dsf-12 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libblkid1_2.17.2-3.2 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-6 libc-dev-bin_2.11.2-6 libc6_2.11.2-6 libc6-dev_2.11.2-6 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdpkg-perl_1.15.8.5 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.4-15 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgomp1_4.4.4-15 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libpam-modules_1.1.1-6 libpam-runtime_1.1.1-6 libpam0g_1.1.1-6 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libss2_1.41.12-2 libstdc++6_4.4.4-15 libstdc++6-4.4-dev_4.4.4-15 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_2:0.1.12-16 libuuid1_2.17.2-3.2 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-23 login_1:4.1.4.2+svn3283-1 lsb-base_3.2-24 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.2 ncurses-base_5.7+20100313-3 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-1 patch_2.6-3 perl_5.10.1-14 perl-base_5.10.1-14 perl-modules_5.10.1-14 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sudo_1.7.4p4-2 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010l-1 util-linux_2.17.2-3.2 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -209,12 +209,12 @@ Unpack source
dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::quilt
gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Wed Nov 17 11:36:23 2010 UTC using RSA key ID 2295D502
+gpgv: Signature made Fri Dec 3 06:37:23 2010 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.10-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.10
-dpkg-source: info: unpacking samtools_0.1.10.orig.tar.bz2
-dpkg-source: info: unpacking samtools_0.1.10-1.debian.tar.gz
+dpkg-source: warning: failed to verify signature on ./samtools_0.1.12a-1.dsc
+dpkg-source: info: extracting samtools in samtools-0.1.12a
+dpkg-source: info: unpacking samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: unpacking samtools_0.1.12a-1.debian.tar.gz
Check disc space
────────────────
@@ -229,34 +229,35 @@ 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 0.1.10-1
- dpkg-source --before-build samtools-0.1.10
+dpkg-buildpackage: source version 0.1.12a-1
+ dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture mips
/usr/bin/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 -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/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 `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long wgsim *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
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
debian/rules build
test -x debian/rules
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
@@ -282,8 +283,8 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.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 knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
@@ -294,10 +295,10 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -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 `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_maqcns.c -o bam_maqcns.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
@@ -314,24 +315,24 @@ gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSE
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
gcc -g -O2 -g -Wall -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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
gcc -g -O2 -g -Wall -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 libbam.a -lm -lcurses -lz -Lbcftools -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
gcc -g -O2 -g -Wall -O2 -fPIC -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -DMD5SUM_MAIN -o md5sum-lite.o md5.c
gcc -g -O2 -g -Wall -O2 -fPIC -o md5sum-lite md5sum-lite.o
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
@@ -341,14 +342,14 @@ gcc -g -O2 -g -Wall -O2 -fPIC -o maq2sam-short maq2sam.c -lz
gcc -g -O2 -g -Wall -O2 -fPIC -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. wgsim.c -o wgsim.o
gcc -g -O2 -g -Wall -O2 -fPIC -o wgsim wgsim.o -lm
-make[2]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/misc'
gcc -c -g -O2 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
gcc -g -O2 -g -Wall -O2 -fPIC -o razip razf.o razip.o knetfile.o -lz
make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a'
touch debian/stamp-makefile-build
/usr/bin/make -C . CFLAGS="-g -O2 -g -Wall -O2 -fPIC" CXXFLAGS="-g -O2 -g -Wall -O2" CPPFLAGS="" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/examples'
../samtools faidx ex1.fa
../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
@@ -377,7 +378,7 @@ gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -lm -lz -L.. -lbam
# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary-arch
test -x debian/rules
@@ -385,6 +386,7 @@ dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
+/usr/share/cdbs/1/rules/buildcore.mk:104: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
Adding cdbs dependencies to debian/samtools.substvars
dh_installdirs -psamtools
@@ -409,8 +411,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/man/man1/bcftools.1.gz
dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
dh_installexamples -plibbam-dev
dh_installman -plibbam-dev
@@ -434,7 +436,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.10-1-mips-Tg8JD2/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.12a-1-mips-QwKHhy/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -448,28 +450,28 @@ dh_shlibdeps -plibbam-dev
dh_gencontrol -psamtools
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
dh_md5sums -psamtools
-dh_builddeb -psamtools
-dpkg-deb: building package `samtools' in `../samtools_0.1.10-1_mips.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-1_mips.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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_mips.deb'.
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_mips.deb'.
dpkg-genchanges -B
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101118-0845
+Build finished at 20101204-0749
-samtools_0.1.10-1_mips.changes:
+samtools_0.1.12a-1_mips.changes:
Format: 1.8
-Date: Wed, 17 Nov 2010 20:32:40 +0900
+Date: Fri, 03 Dec 2010 13:32:21 +0900
Source: samtools
Binary: samtools libbam-dev
Architecture: mips
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: Debian Build Daemon <buildd_mips-ball at buildd...>
@@ -478,36 +480,39 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) unstable; urgency=low
+ samtools (0.1.12a-1) unstable; urgency=low
.
* New upstream release.
+ * Use bzip2 compression for the binary packages (debian/rules).
+ * Incremented debhelper compatibility level to 8, in case ‘--‘ is not
+ available in earlier versions (debian/compat, debian/control).
Checksums-Sha1:
- 91b18f69b3472ed9cb8ca63ac969207792a96111 585154 samtools_0.1.10-1_mips.deb
- 01a953be595d2aa1a7818282a22645f566e54298 182112 libbam-dev_0.1.10-1_mips.deb
+ 819ca6a39882f43c04698bc7aaaa06631ed10e0b 574528 samtools_0.1.12a-1_mips.deb
+ 67683aff48ff5b969fe894fb62879a6a270e2a1d 172934 libbam-dev_0.1.12a-1_mips.deb
Checksums-Sha256:
- 393625a5e362ebccf51ca7712b2d7495d88efd29ca42ad427bf82383dda10b83 585154 samtools_0.1.10-1_mips.deb
- 18d45b59e94cea5cd6033613025ff87da541b3e277c0bea6d0f5b248ef50e314 182112 libbam-dev_0.1.10-1_mips.deb
+ 0558c06b947bd330216871469e3921cc71144f216eba89a26325ff9e62e8efdb 574528 samtools_0.1.12a-1_mips.deb
+ 2fff24c10a6abce81214d6eb3c3973b8a01659ce2a4cbba55edb565f84f96049 172934 libbam-dev_0.1.12a-1_mips.deb
Files:
- c932c08bfb17e566c3d717c11b6cbc22 585154 science optional samtools_0.1.10-1_mips.deb
- e2662d646ba35be2603b795afbb34ff0 182112 libdevel optional libbam-dev_0.1.10-1_mips.deb
+ ad86bf07ab4b83c8e247ce25aa58ce23 574528 science optional samtools_0.1.12a-1_mips.deb
+ 713b2da1c6a306a68ca29dd52f92c7b8 172934 libdevel optional libbam-dev_0.1.12a-1_mips.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_mips.deb
-──────────────────────────
+samtools_0.1.12a-1_mips.deb
+───────────────────────────
new debian package, version 2.0.
- size 585154 bytes: control archive= 1795 bytes.
- 791 bytes, 16 lines control
+ size 574528 bytes: control archive= 1790 bytes.
+ 792 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
- Installed-Size: 1112
+ Installed-Size: 1116
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -520,31 +525,31 @@ samtools_0.1.10-1_mips.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 2010-11-18 08:45 ./
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/samtools/
--rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-18 08:45 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 1031 2010-11-17 11:21 ./usr/share/doc/samtools/README.Debian
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-04 07:49 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 1031 2010-12-03 05:06 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/samtools/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 126609 2010-11-18 08:44 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2010-12-04 07:48 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 764 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.sam
-rw-r--r-- root/root 3225 2010-11-17 04:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 886 2010-11-17 04:16 ./usr/share/doc/samtools/examples/00README.txt
-rw-r--r-- root/root 98 2010-11-17 04:16 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 592 2010-11-17 11:21 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/man/man1/
--rw-r--r-- root/root 7544 2010-11-18 08:45 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2010-11-18 08:45 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/samtools/
+-rw-r--r-- root/root 592 2010-12-03 05:06 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/man/man1/
+-rw-r--r-- root/root 7546 2010-12-04 07:49 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 430 2010-12-04 07:49 ./usr/share/man/man1/razip.1.gz
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/samtools/
-rwxr-xr-x root/root 2415 2010-11-17 04:16 ./usr/share/samtools/blast2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 04:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 5989 2010-11-17 04:16 ./usr/share/samtools/novo2sam.pl
@@ -552,37 +557,37 @@ drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/samtools/
-rwxr-xr-x root/root 2696 2010-11-17 04:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 04:16 ./usr/share/samtools/psl2sam.pl
-rwxr-xr-x root/root 14299 2010-11-17 04:16 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 5778 2010-11-18 08:45 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2010-12-04 07:49 ./usr/share/samtools/varfilter.py
-rwxr-xr-x root/root 15255 2010-11-17 04:16 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 11934 2010-11-17 04:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 12567 2010-12-02 16:41 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 7881 2010-11-17 04:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 3224 2010-11-17 04:16 ./usr/share/samtools/bcf-fix.pl
-rwxr-xr-x root/root 2397 2010-11-17 04:16 ./usr/share/samtools/zoom2sam.pl
-rwxr-xr-x root/root 2729 2010-11-17 04:16 ./usr/share/samtools/wgsim_eval.pl
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/bin/
--rwxr-xr-x root/root 30616 2010-11-18 08:45 ./usr/bin/razip
--rwxr-xr-x root/root 410760 2010-11-18 08:45 ./usr/bin/samtools
--rwxr-xr-x root/root 108636 2010-11-18 08:45 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/samtools/
--rwxr-xr-x root/root 19928 2010-11-18 08:45 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9768 2010-11-18 08:45 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 7764 2010-11-18 08:45 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13268 2010-11-18 08:45 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 7764 2010-11-18 08:45 ./usr/lib/samtools/maq2sam-short
-lrwxrwxrwx root/root 0 2010-11-18 08:45 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.10-1_mips.deb
-────────────────────────────
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/bin/
+-rwxr-xr-x root/root 30712 2010-12-04 07:49 ./usr/bin/razip
+-rwxr-xr-x root/root 410760 2010-12-04 07:49 ./usr/bin/samtools
+-rwxr-xr-x root/root 108704 2010-12-04 07:49 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/samtools/
+-rwxr-xr-x root/root 19928 2010-12-04 07:49 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 9768 2010-12-04 07:49 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 13268 2010-12-04 07:49 ./usr/lib/samtools/md5fa
+-rwxr-xr-x root/root 7764 2010-12-04 07:49 ./usr/lib/samtools/maq2sam-short
+lrwxrwxrwx root/root 0 2010-12-04 07:49 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+
+
+libbam-dev_0.1.12a-1_mips.deb
+─────────────────────────────
new debian package, version 2.0.
- size 182112 bytes: control archive= 893 bytes.
- 673 bytes, 15 lines control
+ size 172934 bytes: control archive= 900 bytes.
+ 674 bytes, 15 lines control
618 bytes, 10 lines md5sums
Package: libbam-dev
Source: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: mips
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists...>
Installed-Size: 448
@@ -596,23 +601,23 @@ libbam-dev_0.1.10-1_mips.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 4925 2010-11-17 11:27 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 29821 2010-11-17 04:16 ./usr/share/doc/libbam-dev/changelog.gz
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 4927 2010-12-03 05:06 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 03:17 ./usr/share/doc/libbam-dev/changelog.gz
-rw-r--r-- root/root 916 2010-11-17 04:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 6101 2010-11-17 04:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 1008 2010-11-17 11:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/include/
+-rw-r--r-- root/root 6692 2010-12-02 21:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 1128 2010-12-03 05:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/include/
-rw-r--r-- root/root 4599 2010-11-17 04:16 ./usr/include/bgzf.h
-rw-r--r-- root/root 3188 2010-11-17 04:16 ./usr/include/faidx.h
-rw-r--r-- root/root 16522 2010-11-17 04:16 ./usr/include/khash.h
-rw-r--r-- root/root 24124 2010-11-17 04:16 ./usr/include/bam.h
-drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/
--rw-r--r-- root/root 303282 2010-11-18 08:45 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-04 07:49 ./usr/lib/
+-rw-r--r-- root/root 303238 2010-12-04 07:49 ./usr/lib/libbam.a
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -621,10 +626,10 @@ drwxr-xr-x root/root 0 2010-11-18 08:45 ./usr/lib/
Built successfully
────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-mips-sbuild-b522fcbb-8ede-4893-98db-96e883e922ef/build/buildd-samtools_0.1.10-1-mips-Tg8JD2
+Purging /var/lib/schroot/mount/sid-mips-sbuild-f75c9a7d-199d-45ad-ba56-a30973cbabf2/build/buildd-samtools_0.1.12a-1-mips-QwKHhy
Not removing build depends: cloned chroot in use
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101118-0845
-Build needed 00:07:09, 9300k disc space
+Finished at 20101204-0749
+Build needed 00:06:58, 9308k disc space
</pre><address><a href="http://trac.cyberhqz.com/wanna-peruse/">wanna-peruse 2.0</a></address></body></html>
--
Processing of sequence alignments in SAM and BAM formats.
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