[med-svn] [SCM] Processing of sequence alignments in SAM and BAM formats. branch, meta, updated. 116e19c49a20aba7acb9eee37b2e6e11e7b92ea9
Charles Plessy
plessy at debian.org
Fri Dec 3 08:41:28 UTC 2010
The following commit has been merged in the meta branch:
commit 116e19c49a20aba7acb9eee37b2e6e11e7b92ea9
Author: Charles Plessy <plessy at debian.org>
Date: Fri Dec 3 17:33:16 2010 +0900
# Uploaded version 0.1.12a-1 for amd64.
diff --git a/amd64.build b/amd64.build
index 95e9934..3ad7398 100644
--- a/amd64.build
+++ b/amd64.build
@@ -1,12 +1,12 @@
sbuild (Debian sbuild) 0.60.5 (14 Nov 2010) on anx178.gsc.riken.jp
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.10-1 (amd64) 17 Nov 2010 20:34 ║
+║ samtools 0.1.12a-1 (amd64) 03 Dec 2010 15:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 0.1.10-1
-Source Version: 0.1.10-1
+Version: 0.1.12a-1
+Source Version: 0.1.12a-1
Architecture: amd64
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -17,7 +17,7 @@ Architecture: amd64
Local sources
─────────────
-samtools_0.1.10-1.dsc exists in .; copying to chroot
+samtools_0.1.12a-1.dsc exists in .; copying to chroot
Check arch
──────────
@@ -30,7 +30,7 @@ Check arch
Build-Depends: build-essential, fakeroot
Checking for already installed dependencies...
build-essential: already installed (11.5)
-fakeroot: already installed (1.14.4-1)
+fakeroot: already installed (1.14.4-2)
Checking for dependency conflicts...
Installing positive dependencies:
Reading package lists...
@@ -48,37 +48,37 @@ Checking correctness of dependencies...
│ Install samtools build dependencies (internal resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
-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 (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+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
Checking for already installed dependencies...
-base-files: already installed (5.9)
+base-files: already installed (5.10)
base-passwd: already installed (3.5.22)
bash: already installed (4.1-3)
coreutils: already installed (8.5-1)
-dash: already installed (0.5.5.1-7.1)
-debianutils: already installed (3.4.1)
+dash: already installed (0.5.5.1-7.3)
+debianutils: already installed (3.4.2)
diffutils: already installed (1:3.0-1)
-dpkg: already installed (1.15.8.5)
+dpkg: already installed (1.15.8.6)
e2fsprogs: already installed (1.41.12-2)
findutils: already installed (4.4.2-1+b1)
grep: already installed (2.6.3-3)
gzip: already installed (1.3.12-9)
-hostname: already installed (3.04)
+hostname: already installed (3.05)
ncurses-base: already installed (5.7+20100313-4)
ncurses-bin: already installed (5.7+20100313-4)
-perl-base: already installed (5.10.1-15)
-sed: already installed (4.2.1-7)
+perl-base: already installed (5.10.1-16)
+sed: already installed (4.2.1-8)
login: already installed (1:4.1.4.2+svn3283-2)
-sysvinit-utils: already installed (2.88dsf-12)
-sysvinit: already installed (2.88dsf-12)
-tar: already installed (1.23-3)
+sysvinit-utils: already installed (2.88dsf-13)
+sysvinit: already installed (2.88dsf-13)
+tar: already installed (1.25-2)
bsdutils: already installed (1:2.17.2-3.3)
mount: already installed (2.17.2-3.3)
util-linux: already installed (2.17.2-3.3)
-libc6-dev: already installed (2.11.2-6)
+libc6-dev: already installed (2.11.2-7)
gcc: already installed (4:4.4.5-1 >= 4:4.4.3 is satisfied)
g++: already installed (4:4.4.5-1 >= 4:4.4.3 is satisfied)
make: already installed (3.81-8)
-dpkg-dev: already installed (1.15.8.5 >= 1.13.5 is satisfied)
+dpkg-dev: already installed (1.15.8.6 >= 1.13.5 is satisfied)
debhelper: missing
Using default version 8.0.0
cdbs: missing
@@ -105,11 +105,11 @@ The following NEW packages will be installed:
libunistring0 libxml2 man-db po-debconf zlib1g-dev
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/12.0 MB of archives.
-After this operation, 36.1 MB of additional disk space will be used.
+Need to get 0 B/12.1 MB of archives.
+After this operation, 36.2 MB of additional disk space will be used.
Selecting previously deselected package bsdmainutils.
-(Reading database ... 10962 files and directories currently installed.)
-Unpacking bsdmainutils (from .../bsdmainutils_8.0.13_amd64.deb) ...
+(Reading database ... 11035 files and directories currently installed.)
+Unpacking bsdmainutils (from .../bsdmainutils_8.0.17_amd64.deb) ...
Selecting previously deselected package groff-base.
Unpacking groff-base (from .../groff-base_1.20.1-10_amd64.deb) ...
Selecting previously deselected package man-db.
@@ -123,7 +123,7 @@ Unpacking gettext-base (from .../gettext-base_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package libpcre3.
Unpacking libpcre3 (from .../libpcre3_8.02-1.1_amd64.deb) ...
Selecting previously deselected package libxml2.
-Unpacking libxml2 (from .../libxml2_2.7.7.dfsg-4_amd64.deb) ...
+Unpacking libxml2 (from .../libxml2_2.7.8.dfsg-1_amd64.deb) ...
Selecting previously deselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_amd64.deb) ...
Selecting previously deselected package libglib2.0-0.
@@ -137,7 +137,7 @@ Unpacking gettext (from .../gettext_0.18.1.1-3_amd64.deb) ...
Selecting previously deselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously deselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16_all.deb) ...
+Unpacking po-debconf (from .../po-debconf_1.0.16+nmu1_all.deb) ...
Selecting previously deselected package debhelper.
Unpacking debhelper (from .../debhelper_8.0.0_all.deb) ...
Selecting previously deselected package cdbs.
@@ -146,7 +146,7 @@ Selecting previously deselected package libncurses5-dev.
Unpacking libncurses5-dev (from .../libncurses5-dev_5.7+20100313-4_amd64.deb) ...
Selecting previously deselected package zlib1g-dev.
Unpacking zlib1g-dev (from .../zlib1g-dev_1%3a1.2.3.4.dfsg-3_amd64.deb) ...
-Setting up bsdmainutils (8.0.13) ...
+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) ...
@@ -156,14 +156,14 @@ Setting up libmagic1 (5.04-5) ...
Setting up file (5.04-5) ...
Setting up gettext-base (0.18.1.1-3) ...
Setting up libpcre3 (8.02-1.1) ...
-Setting up libxml2 (2.7.7.dfsg-4) ...
+Setting up libxml2 (2.7.8.dfsg-1) ...
Setting up html2text (1.3.2a-15) ...
Setting up libglib2.0-0 (2.24.2-1) ...
Setting up libcroco3 (0.6.2-1) ...
Setting up libunistring0 (0.9.3-3) ...
Setting up gettext (0.18.1.1-3) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16) ...
+Setting up po-debconf (1.0.16+nmu1) ...
Setting up debhelper (8.0.0) ...
Setting up cdbs (0.4.89) ...
Setting up libncurses5-dev (5.7+20100313-4) ...
@@ -175,8 +175,8 @@ Reading state information...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Checking correctness of dependencies...
Kernel: Linux 2.6.32-trunk-vserver-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.20.1-15 dpkg-dev_1.15.8.5 g++-4.4_4.4.5-5 gcc-4.4_4.4.5-5 libc6-dev_2.11.2-6 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 linux-libc-dev_2.6.32-26
-Package versions: adduser_3.112+nmu1 apt_0.8.7 base-files_5.9 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.13 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-5 dash_0.5.5.1-7.1 dbus_1.2.24-3 debconf_1.5.36 debconf-i18n_1.5.36 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+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-5 gcc_4:4.4.5-1 gcc-4.4_4.4.5-5 gcc-4.4-base_4.4.5-5 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 java-common_0.40 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libavahi-client3_0.6.27-2 libavahi-common-data_0.6.27-2 libavahi-common3_0.6.27-2 libblkid1_2.17.2-3.3 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 libcups2_1.4.4-6 libdb4.7_4.7.25-9 libdb4.8_4.8.30-2 libdbus-1-3_1.2.24-3 libdpkg-perl_1.15.8.5 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-5 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-5 libgpg-error0_1.6-1 libgssapi-krb5-2_1.8.3+dfsg-2 libk5crypto3_1.8.3+dfsg-2 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-2 libkrb5support0_1.8.3+dfsg-2 liblocale-gettext-perl_1.05-6 liblzma2_4.999.9beta+20100810-1 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libnspr4-0d_4.8.6-1 libnss3-1d_3.12.8-1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-5 libstdc++6-4.4-dev_4.4.5-5 libtasn1-3_2.7-1 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 libunwind7_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.7.dfsg-4 linux-libc-dev_2.6.32-26 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-15 perl-base_5.10.1-15 perl-modules_5.10.1-15 po-debconf_1.0.16 readline-common_6.1-3 sed_4.2.1-7 sensible-utils_0.0.4 sysv-rc_2.88dsf-12 sysvinit_2.88dsf-12 sysvinit-utils_2.88dsf-12 tar_1.23-3 tzdata_2010m-1 tzdata-java_2010m-1 util-linux_2.17.2-3.3 xz-utils_4.999.9beta+20100810-1 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
+Toolchain package versions: binutils_2.20.1-15 dpkg-dev_1.15.8.6 g++-4.4_4.4.5-10 gcc-4.4_4.4.5-10 libc6-dev_2.11.2-7 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 linux-libc-dev_2.6.32-28
+Package versions: adduser_3.112+nmu2 apt_0.8.10 base-files_5.10 base-passwd_3.5.22 bash_4.1-3 binutils_2.20.1-15 bsdmainutils_8.0.17 bsdutils_1:2.17.2-3.3 build-essential_11.5 bzip2_1.0.5-6 cdbs_0.4.89 coreutils_8.5-1 cpp_4:4.4.5-1 cpp-4.4_4.4.5-10 dash_0.5.5.1-7.3 dbus_1.2.24-3 debconf_1.5.37 debconf-i18n_1.5.37 debfoster_2.7-1.1 debhelper_8.0.0 debian-archive-keyring_2010.08.28 debianutils_3.4.2 diffutils_1:3.0-1 dpkg_1.15.8.6 dpkg-dev_1.15.8.6 e2fslibs_1.41.12-2 e2fsprogs_1.41.12-2 fakeroot_1.14.4-2 file_5.04-5 findutils_4.4.2-1+b1 g++_4:4.4.5-1 g++-4.4_4.4.5-10 gcc_4:4.4.5-1 gcc-4.4_4.4.5-10 gcc-4.4-base_4.4.5-10 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_3.05 html2text_1.3.2a-15 initscripts_2.88dsf-13 insserv_1.14.0-2 intltool-debian_0.35.0+20060710.1 java-common_0.40 libacl1_2.2.49-4 libattr1_1:2.4.44-2 libavahi-client3_0.6.27-3 libavahi-common-data_0.6.27-3 libavahi-common3_0.6.27-3 libblkid1_2.17.2-3.3 libbz2-1.0_1.0.5-6 libc-bin_2.11.2-7 libc-dev-bin_2.11.2-7 libc6_2.11.2-7 libc6-dev_2.11.2-7 libcomerr2_1.41.12-2 libcroco3_0.6.2-1 libcups2_1.4.4-7 libdb4.7_4.7.25-10 libdb4.8_4.8.30-3 libdbus-1-3_1.2.24-3 libdpkg-perl_1.15.8.6 libexpat1_2.0.1-7 libgc1c2_1:6.8-1.2 libgcc1_1:4.4.5-10 libgcrypt11_1.4.5-2 libgdbm3_1.8.3-9 libglib2.0-0_2.24.2-1 libgmp3c2_2:4.3.2+dfsg-1 libgnutls26_2.8.6-1 libgomp1_4.4.5-10 libgpg-error0_1.6-1 libgssapi-krb5-2_1.8.3+dfsg-3 libk5crypto3_1.8.3+dfsg-3 libkeyutils1_1.4-1 libkrb5-3_1.8.3+dfsg-3 libkrb5support0_1.8.3+dfsg-3 liblocale-gettext-perl_1.05-6 liblzma2_5.0.0-2 libmagic1_5.04-5 libmpfr1ldbl_2.4.2-3 libmpfr4_3.0.0-2 libncurses5_5.7+20100313-4 libncurses5-dev_5.7+20100313-4 libnspr4-0d_4.8.6-1 libnss3-1d_3.12.8-1 libpam-modules_1.1.1-6.1 libpam-runtime_1.1.1-6.1 libpam0g_1.1.1-6.1 libpcre3_8.02-1.1 libreadline6_6.1-3 libselinux1_2.0.96-1 libsepol1_2.0.41-1 libslang2_2.2.2-4 libsqlite3-0_3.7.3-1 libss2_1.41.12-2 libstdc++6_4.4.5-10 libstdc++6-4.4-dev_4.4.5-10 libtasn1-3_2.7-1 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 libunwind7_0.99-0.2 libusb-0.1-4_2:0.1.12-16 libuuid1_2.17.2-3.3 libxml2_2.7.8.dfsg-1 linux-libc-dev_2.6.32-28 login_1:4.1.4.2+svn3283-2 lsb-base_3.2-26 lzma_4.43-14 make_3.81-8 man-db_2.5.7-6 mawk_1.3.3-15 mount_2.17.2-3.3 ncurses-base_5.7+20100313-4 ncurses-bin_5.7+20100313-4 passwd_1:4.1.4.2+svn3283-2 patch_2.6-3 perl_5.10.1-16 perl-base_5.10.1-16 perl-modules_5.10.1-16 po-debconf_1.0.16+nmu1 readline-common_6.1-3 sed_4.2.1-8 sensible-utils_0.0.6 sysv-rc_2.88dsf-13 sysvinit_2.88dsf-13 sysvinit-utils_2.88dsf-13 tar_1.25-2 tzdata_2010o-1 tzdata-java_2010o-1 util-linux_2.17.2-3.3 xz-utils_5.0.0-2 zlib1g_1:1.2.3.4.dfsg-3 zlib1g-dev_1:1.2.3.4.dfsg-3
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -186,10 +186,10 @@ Package versions: adduser_3.112+nmu1 apt_0.8.7 base-files_5.9 base-passwd_3.5.22
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (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: extracting unsigned source package (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
────────────────
@@ -204,40 +204,41 @@ 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-buildpackage: source version 0.1.12a-1
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-0.1.10
+ dpkg-source --before-build samtools-0.1.12a
dpkg-buildpackage: host architecture amd64
/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
+make[1]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
-make[1]: Leaving directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/misc'
+make[1]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
- dpkg-source -b samtools-0.1.10
+ dpkg-source -b samtools-0.1.12a
dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_0.1.10.orig.tar.bz2
-dpkg-source: info: building samtools in samtools_0.1.10-1.debian.tar.gz
-dpkg-source: info: building samtools in samtools_0.1.10-1.dsc
+dpkg-source: info: building samtools using existing ./samtools_0.1.12a.orig.tar.bz2
+dpkg-source: info: building samtools in samtools_0.1.12a-1.debian.tar.gz
+dpkg-source: info: building samtools in samtools_0.1.12a-1.dsc
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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
+make[1]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
@@ -257,8 +258,8 @@ 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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
@@ -269,10 +270,10 @@ 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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/misc'
make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
@@ -289,24 +290,24 @@ 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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[3]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[3]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[3]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
+make[3]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[3]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/bcftools'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
-make[3]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/bcftools'
+make[3]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/misc'
make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[3]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/bcftools'
-make[2]: Entering directory `/build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/bcftools'
+make[2]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
@@ -316,14 +317,14 @@ 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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/misc'
+make[2]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10'
+make[1]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/examples'
+make[1]: Entering directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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.
@@ -352,7 +353,7 @@ 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/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/examples'
+make[1]: Leaving directory `/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/examples'
touch debian/stamp-makefile-check
/usr/bin/fakeroot debian/rules binary
test -x debian/rules
@@ -360,6 +361,7 @@ 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
@@ -384,8 +386,8 @@ dh_lintian -psamtools
dh_install -psamtools
dh_link -psamtools
dh_installmime -psamtools
-install -m 644 bcftools/README /build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/debian/samtools/usr/share/man/man1/bcftools.1.gz
+install -m 644 bcftools/README /build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/debian/samtools/usr/share/doc/samtools/README.bcftools
+ln -s samtools.1.gz /build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/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
@@ -409,7 +411,7 @@ dh_strip -psamtools
dh_compress -psamtools
dh_fixperms -psamtools
dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/charles-samtools_0.1.10-1-amd64-EzlFO6/samtools-0.1.10/debian/samtools/usr/share/samtools/varfilter.py
+sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/charles-samtools_0.1.12a-1-amd64-dvGJbJ/samtools-0.1.12a/debian/samtools/usr/share/samtools/varfilter.py
dh_strip -plibbam-dev
dh_compress -plibbam-dev
dh_fixperms -plibbam-dev
@@ -423,27 +425,27 @@ 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_amd64.deb'.
+dh_builddeb -psamtools -- -Z=bzip2
+dpkg-deb: building package `samtools' in `../samtools_0.1.12a-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
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.10-1_amd64.deb'.
- dpkg-genchanges >../samtools_0.1.10-1_amd64.changes
+dh_builddeb -plibbam-dev -- -Z=bzip2
+dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.12a-1_amd64.deb'.
+ dpkg-genchanges >../samtools_0.1.12a-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-0.1.10
+ dpkg-source --after-build samtools-0.1.12a
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20101117-2035
+Build finished at 20101203-1525
-samtools_0.1.10-1_amd64.changes:
+samtools_0.1.12a-1_amd64.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: source amd64
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -452,45 +454,48 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) 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:
- 52802d5931584725fb72071c388d9675cc9e4448 1053 samtools_0.1.10-1.dsc
- 02bb93a23f1bb13ab8fd87cc24d3a9f82ead0775 353190 samtools_0.1.10.orig.tar.bz2
- 3244f135ec4f5341efb9ceaa61c3df80a8622c7e 6332 samtools_0.1.10-1.debian.tar.gz
- 337553017fbf3c053ac244ee7a5c41a583f8a91c 558002 samtools_0.1.10-1_amd64.deb
- 0e21cce7f456b610a6db9fa59e381e0e5729d090 164276 libbam-dev_0.1.10-1_amd64.deb
+ d28a39c61a44ebe0edb450933c8e8e0427c39c9c 1060 samtools_0.1.12a-1.dsc
+ d517cd189aa714251a0e43cb83dea3ae0f29bffa 355633 samtools_0.1.12a.orig.tar.bz2
+ 1714e415bbfb7f6c2141205ef2ca24e04cb64104 6337 samtools_0.1.12a-1.debian.tar.gz
+ 6eb40ab90ecb10e909dfd60554c2026ba85e09e2 553878 samtools_0.1.12a-1_amd64.deb
+ 27451e1b4da49f60d3a8332bdcf728bf5b70db44 155576 libbam-dev_0.1.12a-1_amd64.deb
Checksums-Sha256:
- 9158813830bc779c46d3f8cf0fbb9359a639694bd3eb5549d17883464ec8307a 1053 samtools_0.1.10-1.dsc
- 3b7f4457beace8018f0674d4ab88f573c4bdcf59a1b52c8b476520a135dcec52 353190 samtools_0.1.10.orig.tar.bz2
- 69adab32b94cae93e5f0cdfdf8ee88e002596452208fa53d46820ea1fdc02139 6332 samtools_0.1.10-1.debian.tar.gz
- 2a3c96c8f4d7546a5a04ef8e4c3a1c8b58ce94e7e127542126bbcdbc2424c9f5 558002 samtools_0.1.10-1_amd64.deb
- 0943254694e3d0bc0bc6f0d9c3c54c6e3e19c476b563a043ac4053f172053205 164276 libbam-dev_0.1.10-1_amd64.deb
+ 1f3a937b0d45a83781563020b6ffff0549e406d05b7260b994d65ab26784f268 1060 samtools_0.1.12a-1.dsc
+ 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac 355633 samtools_0.1.12a.orig.tar.bz2
+ 28e9888d37009876fb4cfa86d64402617688513ae6fafe596b0ca7c02a33c983 6337 samtools_0.1.12a-1.debian.tar.gz
+ 97af218314a6febe86b1754c25b594c2b5380eda00ad321e5f6b509eb298dbc9 553878 samtools_0.1.12a-1_amd64.deb
+ dcb266f7a1a40b8ec8cb437f0e6dede7f0bce9d026d9f61a873fb59dc760b7fc 155576 libbam-dev_0.1.12a-1_amd64.deb
Files:
- 9cbc62536daa5d785c75a036f1662ceb 1053 science optional samtools_0.1.10-1.dsc
- 30c707361d130528421820b851c7771f 353190 science optional samtools_0.1.10.orig.tar.bz2
- 1f3d74deb42af5015db1e1f3ede2615f 6332 science optional samtools_0.1.10-1.debian.tar.gz
- ccc6f5a4f37892bb49e1d503160e1ba1 558002 science optional samtools_0.1.10-1_amd64.deb
- f229835979dfb8b3759352da98ed25c0 164276 libdevel optional libbam-dev_0.1.10-1_amd64.deb
+ 8c73291bd06376a32406b53f79cd68ec 1060 science optional samtools_0.1.12a-1.dsc
+ 500ae32fb431de3940e0e955744b9b36 355633 science optional samtools_0.1.12a.orig.tar.bz2
+ 0a8fee2b3be6402a6031b41723480c93 6337 science optional samtools_0.1.12a-1.debian.tar.gz
+ 8ac71647603e1b924e0ccde3284df567 553878 science optional samtools_0.1.12a-1_amd64.deb
+ 40d878a2a6a6afa9970ba8d66d02e072 155576 libdevel optional libbam-dev_0.1.12a-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_0.1.10-1_amd64.deb
-───────────────────────────
+samtools_0.1.12a-1_amd64.deb
+────────────────────────────
new debian package, version 2.0.
- size 558002 bytes: control archive= 1795 bytes.
- 791 bytes, 16 lines control
+ size 553878 bytes: control archive= 1791 bytes.
+ 792 bytes, 16 lines control
2517 bytes, 38 lines md5sums
Package: samtools
- Version: 0.1.10-1
+ Version: 0.1.12a-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 988
+ Installed-Size: 992
Depends: libc6 (>= 2.7), libncurses5 (>= 5.7+20100313), zlib1g (>= 1:1.2.3.3.dfsg)
Suggests: python
Section: science
@@ -503,24 +508,24 @@ samtools_0.1.10-1_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 2010-11-17 20:35 ./
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/bin/
--rwxr-xr-x root/root 318672 2010-11-17 20:35 ./usr/bin/samtools
--rwxr-xr-x root/root 24792 2010-11-17 20:35 ./usr/bin/razip
--rwxr-xr-x root/root 85384 2010-11-17 20:35 ./usr/bin/bcftools
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/lib/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/lib/samtools/
--rwxr-xr-x root/root 8472 2010-11-17 20:35 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 8184 2010-11-17 20:35 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 19248 2010-11-17 20:35 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 8136 2010-11-17 20:35 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 11680 2010-11-17 20:35 ./usr/lib/samtools/md5fa
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/bin/
+-rwxr-xr-x root/root 318672 2010-12-03 15:25 ./usr/bin/samtools
+-rwxr-xr-x root/root 24832 2010-12-03 15:25 ./usr/bin/razip
+-rwxr-xr-x root/root 85384 2010-12-03 15:25 ./usr/bin/bcftools
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/lib/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/lib/samtools/
+-rwxr-xr-x root/root 8472 2010-12-03 15:25 ./usr/lib/samtools/md5sum-lite
+-rwxr-xr-x root/root 8184 2010-12-03 15:25 ./usr/lib/samtools/maq2sam-long
+-rwxr-xr-x root/root 19248 2010-12-03 15:25 ./usr/lib/samtools/wgsim
+-rwxr-xr-x root/root 8136 2010-12-03 15:25 ./usr/lib/samtools/maq2sam-short
+-rwxr-xr-x root/root 11680 2010-12-03 15:25 ./usr/lib/samtools/md5fa
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./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 11934 2010-11-17 13:16 ./usr/share/samtools/vcfutils.pl
+-rwxr-xr-x root/root 12567 2010-12-03 01:41 ./usr/share/samtools/vcfutils.pl
-rwxr-xr-x root/root 7881 2010-11-17 13:16 ./usr/share/samtools/sam2vcf.pl
-rwxr-xr-x root/root 2696 2010-11-17 13:16 ./usr/share/samtools/soap2sam.pl
-rwxr-xr-x root/root 2397 2010-11-17 13:16 ./usr/share/samtools/zoom2sam.pl
@@ -529,43 +534,43 @@ drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/samtools/
-rwxr-xr-x root/root 15255 2010-11-17 13:16 ./usr/share/samtools/export2sam.pl
-rwxr-xr-x root/root 2112 2010-11-17 13:16 ./usr/share/samtools/bowtie2sam.pl
-rwxr-xr-x root/root 2022 2010-11-17 13:16 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2010-11-17 20:35 ./usr/share/samtools/varfilter.py
+-rwxr-xr-x root/root 5778 2010-12-03 15:25 ./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 3224 2010-11-17 13:16 ./usr/share/samtools/bcf-fix.pl
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1008 2010-11-17 20:32 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 1128 2010-12-03 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2010-11-17 20:21 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2010-11-17 20:21 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 29821 2010-11-17 13:16 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2010-11-17 20:35 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 6101 2010-11-17 13:16 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/doc/samtools/examples/
+-rw-r--r-- root/root 592 2010-12-03 14:06 ./usr/share/doc/samtools/reference
+-rw-r--r-- root/root 1031 2010-12-03 14:06 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 30752 2010-11-22 12:17 ./usr/share/doc/samtools/changelog.gz
+-rw-r--r-- root/root 1966 2010-12-03 15:25 ./usr/share/doc/samtools/README.bcftools
+-rw-r--r-- root/root 6692 2010-12-03 06:16 ./usr/share/doc/samtools/NEWS.gz
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/doc/samtools/examples/
-rw-r--r-- root/root 114565 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.sam.gz
-rw-r--r-- root/root 3225 2010-11-17 13:16 ./usr/share/doc/samtools/examples/ex1.fa
-rw-r--r-- root/root 764 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126609 2010-11-17 20:35 ./usr/share/doc/samtools/examples/ex1.bam.gz
+-rw-r--r-- root/root 126609 2010-12-03 15:25 ./usr/share/doc/samtools/examples/ex1.bam.gz
-rw-r--r-- root/root 98 2010-11-17 13:16 ./usr/share/doc/samtools/examples/toy.fa
-rw-r--r-- root/root 886 2010-11-17 13:16 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 4925 2010-11-17 20:27 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/man/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2010-11-17 20:35 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 7544 2010-11-17 20:35 ./usr/share/man/man1/samtools.1.gz
-lrwxrwxrwx root/root 0 2010-11-17 20:35 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
+-rw-r--r-- root/root 4927 2010-12-03 14:06 ./usr/share/doc/samtools/copyright
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 430 2010-12-03 15:25 ./usr/share/man/man1/razip.1.gz
+-rw-r--r-- root/root 7546 2010-12-03 15:25 ./usr/share/man/man1/samtools.1.gz
+lrwxrwxrwx root/root 0 2010-12-03 15:25 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-libbam-dev_0.1.10-1_amd64.deb
-─────────────────────────────
+libbam-dev_0.1.12a-1_amd64.deb
+──────────────────────────────
new debian package, version 2.0.
- size 164276 bytes: control archive= 900 bytes.
- 674 bytes, 15 lines control
+ size 155576 bytes: control archive= 900 bytes.
+ 675 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: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 440
@@ -579,23 +584,23 @@ libbam-dev_0.1.10-1_amd64.deb
sorting, merging, generating pileup, and quickly retrieval of reads overlapped
with a specified region.
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/lib/
--rw-r--r-- root/root 295158 2010-11-17 20:35 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/include/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/lib/
+-rw-r--r-- root/root 295230 2010-12-03 15:25 ./usr/lib/libbam.a
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/include/
-rw-r--r-- root/root 24124 2010-11-17 13:16 ./usr/include/bam.h
-rw-r--r-- root/root 3188 2010-11-17 13:16 ./usr/include/faidx.h
-rw-r--r-- root/root 16522 2010-11-17 13:16 ./usr/include/khash.h
-rw-r--r-- root/root 4599 2010-11-17 13:16 ./usr/include/bgzf.h
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/doc/
-drwxr-xr-x root/root 0 2010-11-17 20:35 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 1008 2010-11-17 20:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2010-12-03 15:25 ./usr/share/doc/libbam-dev/
+-rw-r--r-- root/root 1128 2010-12-03 14:07 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-rw-r--r-- root/root 916 2010-11-17 13:16 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 29821 2010-11-17 13:16 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 6101 2010-11-17 13:16 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 4925 2010-11-17 20:27 ./usr/share/doc/libbam-dev/copyright
+-rw-r--r-- root/root 30752 2010-11-22 12:17 ./usr/share/doc/libbam-dev/changelog.gz
+-rw-r--r-- root/root 6692 2010-12-03 06:16 ./usr/share/doc/libbam-dev/NEWS.gz
+-rw-r--r-- root/root 4927 2010-12-03 14:06 ./usr/share/doc/libbam-dev/copyright
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -609,7 +614,7 @@ Built successfully
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
-Purging /var/lib/schroot/mount/sid-54e747a7-90d4-4905-baef-beed9b35a681/build/charles-samtools_0.1.10-1-amd64-EzlFO6
+Purging /var/lib/schroot/mount/sid-97b0c08f-0cb0-454e-925f-861ff3790c48/build/charles-samtools_0.1.12a-1-amd64-dvGJbJ
Reading package lists...
Building dependency tree...
Reading state information...
@@ -623,8 +628,8 @@ The following packages will be REMOVED:
libncurses5-dev* libpcre3* libunistring0* libxml2* man-db* po-debconf*
zlib1g-dev*
0 upgraded, 0 newly installed, 19 to remove and 0 not upgraded.
-After this operation, 36.1 MB disk space will be freed.
-(Reading database ... 13337 files and directories currently installed.)
+After this operation, 36.2 MB disk space will be freed.
+(Reading database ... 13410 files and directories currently installed.)
Removing cdbs ...
Removing debhelper ...
Removing man-db ...
@@ -660,16 +665,16 @@ Removing zlib1g-dev ...
└──────────────────────────────────────────────────────────────────────────────┘
Architecture: amd64
-Build-Space: 10364
-Build-Time: 20
+Build-Space: 10372
+Build-Time: 21
Distribution: unstable
-Job: samtools_0.1.10-1.dsc
+Job: samtools_0.1.12a-1.dsc
Package: samtools
-Package-Time: 28
-Source-Version: 0.1.10-1
-Space: 10364
+Package-Time: 32
+Source-Version: 0.1.12a-1
+Space: 10372
Status: successful
-Version: 0.1.10-1
+Version: 0.1.12a-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20101117-2035
-Build needed 00:00:28, 10364k disc space
+Finished at 20101203-1525
+Build needed 00:00:32, 10372k disc space
diff --git a/amd64.changes b/amd64.changes
index 64d9bcd..49c8e75 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA256
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: source amd64
-Version: 0.1.10-1
+Version: 0.1.12a-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -15,42 +15,45 @@ Description:
libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
samtools - processing sequence alignments in SAM and BAM formats
Changes:
- samtools (0.1.10-1) 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).
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- 30c707361d130528421820b851c7771f 353190 science optional samtools_0.1.10.orig.tar.bz2
- 1f3d74deb42af5015db1e1f3ede2615f 6332 science optional samtools_0.1.10-1.debian.tar.gz
- ccc6f5a4f37892bb49e1d503160e1ba1 558002 science optional samtools_0.1.10-1_amd64.deb
- f229835979dfb8b3759352da98ed25c0 164276 libdevel optional libbam-dev_0.1.10-1_amd64.deb
+ 4a86a813ee587939bf0e31eef9445299 1946 science optional samtools_0.1.12a-1.dsc
+ 500ae32fb431de3940e0e955744b9b36 355633 science optional samtools_0.1.12a.orig.tar.bz2
+ 0a8fee2b3be6402a6031b41723480c93 6337 science optional samtools_0.1.12a-1.debian.tar.gz
+ 8ac71647603e1b924e0ccde3284df567 553878 science optional samtools_0.1.12a-1_amd64.deb
+ 40d878a2a6a6afa9970ba8d66d02e072 155576 libdevel optional libbam-dev_0.1.12a-1_amd64.deb
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diff --git a/dsc b/dsc
index f974048..484e6e6 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, libbam-dev
Architecture: any
-Version: 0.1.10-1
+Version: 0.1.12a-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>
Dm-Upload-Allowed: yes
@@ -13,31 +13,31 @@ Homepage: http://samtools.sourceforge.net
Standards-Version: 3.9.1
Vcs-Browser: http://git.debian.org/?p=debian-med/samtools.git
Vcs-Git: git://git.debian.org/debian-med/samtools.git
-Build-Depends: debhelper (>= 7), cdbs, libncurses5-dev, zlib1g-dev
+Build-Depends: debhelper (>= 8), cdbs, libncurses5-dev, zlib1g-dev
Checksums-Sha1:
- 02bb93a23f1bb13ab8fd87cc24d3a9f82ead0775 353190 samtools_0.1.10.orig.tar.bz2
- 3244f135ec4f5341efb9ceaa61c3df80a8622c7e 6332 samtools_0.1.10-1.debian.tar.gz
+ d517cd189aa714251a0e43cb83dea3ae0f29bffa 355633 samtools_0.1.12a.orig.tar.bz2
+ 1714e415bbfb7f6c2141205ef2ca24e04cb64104 6337 samtools_0.1.12a-1.debian.tar.gz
Checksums-Sha256:
- 3b7f4457beace8018f0674d4ab88f573c4bdcf59a1b52c8b476520a135dcec52 353190 samtools_0.1.10.orig.tar.bz2
- 69adab32b94cae93e5f0cdfdf8ee88e002596452208fa53d46820ea1fdc02139 6332 samtools_0.1.10-1.debian.tar.gz
+ 377ed5cd2a4bb2b1ad572ca6fcafdd8ed644b67f01ab00fa020618fac11e59ac 355633 samtools_0.1.12a.orig.tar.bz2
+ 28e9888d37009876fb4cfa86d64402617688513ae6fafe596b0ca7c02a33c983 6337 samtools_0.1.12a-1.debian.tar.gz
Files:
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- 1f3d74deb42af5015db1e1f3ede2615f 6332 samtools_0.1.10-1.debian.tar.gz
+ 500ae32fb431de3940e0e955744b9b36 355633 samtools_0.1.12a.orig.tar.bz2
+ 0a8fee2b3be6402a6031b41723480c93 6337 samtools_0.1.12a-1.debian.tar.gz
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--
Processing of sequence alignments in SAM and BAM formats.
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