[med-svn] samtools 01/01: samtools (1.2-1) unstable; urgency=medium
Charles Plessy
plessy at moszumanska.debian.org
Mon Jun 15 22:06:23 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a commit to branch debian/logs/unstable
in repository samtools.
commit dca461d664cedc0659feb9db0bed99a3d9f8dc53
Author: Charles Plessy <plessy at debian.org>
Date: Tue Jun 16 07:06:09 2015 +0900
samtools (1.2-1) unstable; urgency=medium
a5f28a0 Merge tag '1.2' into debian/unstable
c542e84 Build-depend on libhts-dev 1.2.
6c2d9cd Build-depend and recommend libio-pty-perl.
(Needed for the regression tests.)
23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
1091aab Refreshed fuzzy patches.
-- Charles Plessy <plessy at debian.org> Tue, 16 Jun 2015 06:12:12 +0900
---
amd64.changes | 77 ++-
amd64.log | 1865 +++++++++++++++++++++++++++++++--------------------------
dsc | 42 +-
upload | 14 +-
4 files changed, 1081 insertions(+), 917 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index ee4b1f4..e9876d9 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA512
Format: 1.8
-Date: Thu, 25 Sep 2014 09:04:20 +0900
+Date: Tue, 16 Jun 2015 06:12:12 +0900
Source: samtools
Binary: samtools samtools-test
-Architecture: source amd64 all
-Version: 1.1-1
+Architecture: source all amd64
+Version: 1.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -15,48 +15,47 @@ Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package.
Changes:
- samtools (1.1-1) unstable; urgency=medium
+ samtools (1.2-1) unstable; urgency=medium
.
- c448d48 Merge tag '1.1' into debian/unstable
- d12ab1e Merge branch 'develop' into debian/unstable to solve issue
- with regression tests needing a pseudo-terminal.
- See https://github.com/samtools/samtools/issues/300
- c87f8ce Add autopkg tests.
- 7c50b7b Removed python-wrong-path-for-interpreter.patch
- (issue solved upstream).
+ a5f28a0 Merge tag '1.2' into debian/unstable
+ c542e84 Build-depend on libhts-dev 1.2.
+ 6c2d9cd Build-depend and recommend libio-pty-perl.
+ (Needed for the regression tests.)
+ 23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
+ 1091aab Refreshed fuzzy patches.
Checksums-Sha1:
- 388015e08bb5a845321b7658cc55cef2e5613d9e 2104 samtools_1.1-1.dsc
- ca446ec24eabd2f71605dde55a787f182cb50f13 4320951 samtools_1.1.orig.tar.gz
- 0e4de8be00fb4dd375048b1b1dc05e2f120e2ead 10164 samtools_1.1-1.debian.tar.xz
- 3424183e6577c856a09f4f838c1a398c8e5744ba 378168 samtools_1.1-1_amd64.deb
- f2542cc1d07aef31d216d43630c87c9edf38cabd 2644466 samtools-test_1.1-1_all.deb
+ fba84572a2c3f7fc652cfe530bbad24b9957b28f 2117 samtools_1.2-1.dsc
+ 9fabb4903b9d1521aeea8a5538e64aefe8e85526 4318615 samtools_1.2.orig.tar.gz
+ a91e9483810ed9ed0e979138febf467b6db6956d 9596 samtools_1.2-1.debian.tar.xz
+ 5af2830490b1588c6e2bcd3021733c0681cddfb4 2644688 samtools-test_1.2-1_all.deb
+ 5d97f7b4d27954e75904cd4a6155422f65022e57 392492 samtools_1.2-1_amd64.deb
Checksums-Sha256:
- ce8fe3ddb71817ba6d655ed6ac7d667c2d0b3a2664f78ae5fd0382da3fd307b1 2104 samtools_1.1-1.dsc
- cee231e33b7290be8e07dea43a99b885d9df79d957625ac84879b47ff91cda69 4320951 samtools_1.1.orig.tar.gz
- 50e5d2299c2d99ce53647fc0cb08eee53bc31d08bfa7d7cc981e6fae28ab231b 10164 samtools_1.1-1.debian.tar.xz
- 55ca7fb40430ba8c17967568f5c48ee19379bdbae3cb218456dae7fed5ea107d 378168 samtools_1.1-1_amd64.deb
- 5fb20f9d61452c8863e6ff42d2ea0d9ec72211fb9dd43cca3b55eeeb49985196 2644466 samtools-test_1.1-1_all.deb
+ 56421ef07a64a3c54c557dd0d91dcbc7d9b5b08dc204ee09d852949db9900653 2117 samtools_1.2-1.dsc
+ e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47 4318615 samtools_1.2.orig.tar.gz
+ c3a6bead979cd8bb0b8fec3e9d6b2bb352db21ae4fdac8ad214757aed72bad23 9596 samtools_1.2-1.debian.tar.xz
+ 5a3017e37793e4dc1daa7f8c029cb943d98001cd580d110bf569093b0bbb7e2d 2644688 samtools-test_1.2-1_all.deb
+ 5af217333dd6c66de5667be1c7a3edb695f370a5add22458081747a7b8968856 392492 samtools_1.2-1_amd64.deb
Files:
- 1d7d68a126fe90d8366eb3fed809230c 378168 science optional samtools_1.1-1_amd64.deb
- 9ffe69f7310c265243d2fd553c322435 2644466 science optional samtools-test_1.1-1_all.deb
- 148939471e917dfe65acde2ec02d10e0 2104 science optional samtools_1.1-1.dsc
- 5fda5c175d04bff39c56078aea7cd3b1 4320951 science optional samtools_1.1.orig.tar.gz
- 40b3a1f31e22323c8d247e1bff1a9c52 10164 science optional samtools_1.1-1.debian.tar.xz
+ 57b89f47bc3977ee7cbdd2c0edac73b6 2117 science optional samtools_1.2-1.dsc
+ 2748356ef392c0694ca1142de37cf2aa 4318615 science optional samtools_1.2.orig.tar.gz
+ af3dbbae0acff0b7f989b54455839b56 9596 science optional samtools_1.2-1.debian.tar.xz
+ 31a29a2c1ccf9235d4967d0582e25b51 2644688 science optional samtools-test_1.2-1_all.deb
+ d7ce058d6c3b4d64fc6530615c960f6e 392492 science optional samtools_1.2-1_amd64.deb
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diff --git a/amd64.log b/amd64.log
index 3a44ba0..d8368c5 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,20 +1,20 @@
-sbuild (Debian sbuild) 0.64.1 (13 Oct 2013) on aqwa.igloo
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on aqwa.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (amd64) 25 sept. 2014 09:05 ║
+║ samtools 1.2-1 (amd64) 16 juin 2015 06:14 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-1
+Source Version: 1.2-1
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-I: NOTICE: Log filtering will replace 'build/samtools-No0uS_/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-No0uS_' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-3e8fcdc5-336b-4691-bf43-e99b6e156ad7' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-HI9FCU/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-HI9FCU' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/unstable-amd64-sbuild-f5de7d7c-936b-47a6-bda9-e4ff8c4e4fc1' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
@@ -24,7 +24,7 @@ Hit http://ftp.jp.debian.org unstable InRelease
Get:1 http://ftp.jp.debian.org unstable/main Sources/DiffIndex [7876 B]
Get:2 http://ftp.jp.debian.org unstable/main amd64 Packages/DiffIndex [7876 B]
Get:3 http://ftp.jp.debian.org unstable/main Translation-en/DiffIndex [7876 B]
-Fetched 23.6 kB in 1s (12.1 kB/s)
+Fetched 23.6 kB in 1s (12.7 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -39,15 +39,24 @@ Reading state information...
Local sources
─────────────
-samtools_1.1-1.dsc exists in .; copying to chroot
+samtools_1.2-1.dsc exists in .; copying to chroot
-Check arch
-──────────
+Check architectures
+───────────────────
+
+
+Check dependencies
+──────────────────
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-5QNb6M/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-GsDMvZ/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -62,17 +71,22 @@ The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/820 B of archives.
+Need to get 0 B/772 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11169 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-aSqs1T/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11516 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-0gU_bo/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -86,8 +100,8 @@ Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf tabix zlib1g-dev
+ libhts1 libicu52 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
www-browser libmail-box-perl
@@ -98,127 +112,140 @@ Recommended packages:
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
+ libhts1 libicu52 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
+Need to get 910 kB/17.3 MB of archives.
+After this operation, 61.3 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.1 [180 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main libhts1 amd64 1.2.1-1 [229 kB]
+Get:3 http://ftp.jp.debian.org/debian/ unstable/main libhts-dev amd64 1.2.1-1 [278 kB]
+Get:4 http://ftp.jp.debian.org/debian/ unstable/main tabix amd64 1.2.1-1 [223 kB]
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/10.2 MB of archives.
-After this operation, 31.7 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1:amd64.
-(Reading database ... 11169 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_amd64.deb ...
-Unpacking libpipeline1:amd64 (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_amd64.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5_amd64.deb ...
-Unpacking bsdmainutils (9.0.5) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_amd64.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:amd64.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_amd64.deb ...
-Unpacking libasprintf0c2:amd64 (0.19.2-2) ...
-Selecting previously unselected package libmagic1:amd64.
-Preparing to unpack .../libmagic1_1%3a5.19-2_amd64.deb ...
-Unpacking libmagic1:amd64 (1:5.19-2) ...
-Selecting previously unselected package libxml2:amd64.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4_amd64.deb ...
-Unpacking libxml2:amd64 (2.9.1+dfsg1-4) ...
-Selecting previously unselected package libffi6:amd64.
-Preparing to unpack .../libffi6_3.1-2_amd64.deb ...
-Unpacking libffi6:amd64 (3.1-2) ...
-Selecting previously unselected package libglib2.0-0:amd64.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_amd64.deb ...
-Unpacking libglib2.0-0:amd64 (2.42.0-1) ...
-Selecting previously unselected package libcroco3:amd64.
-Preparing to unpack .../libcroco3_0.6.8-3_amd64.deb ...
-Unpacking libcroco3:amd64 (0.6.8-3) ...
-Selecting previously unselected package libhts1:amd64.
-Preparing to unpack .../libhts1_1.1-1_amd64.deb ...
-Unpacking libhts1:amd64 (1.1-1) ...
-Selecting previously unselected package libunistring0:amd64.
-Preparing to unpack .../libunistring0_0.9.3-5.2_amd64.deb ...
-Unpacking libunistring0:amd64 (0.9.3-5.2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_amd64.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_amd64.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_amd64.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:amd64.
-Preparing to unpack .../libhts-dev_1.1-1_amd64.deb ...
-Unpacking libhts-dev:amd64 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:amd64.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_amd64.deb ...
-Unpacking libtinfo-dev:amd64 (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:amd64.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_amd64.deb ...
-Unpacking libncurses5-dev:amd64 (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.1-1_amd64.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:amd64.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_amd64.deb ...
-Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:amd64 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5) ...
-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 man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:amd64 (0.19.2-2) ...
-Setting up libmagic1:amd64 (1:5.19-2) ...
-Setting up libxml2:amd64 (2.9.1+dfsg1-4) ...
-Setting up libffi6:amd64 (3.1-2) ...
-Setting up libglib2.0-0:amd64 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:amd64 (0.6.8-3) ...
-Setting up libhts1:amd64 (1.1-1) ...
-Setting up libunistring0:amd64 (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:amd64 (1.1-1) ...
-Setting up libtinfo-dev:amd64 (5.9+20140913-1) ...
-Setting up libncurses5-dev:amd64 (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Fetched 910 kB in 0s (1474 kB/s)
+Selecting previously unselected package libpipeline1:amd64.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 11516 files and directories currently installed.)
+Preparing to unpack .../libpipeline1_1.4.0-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.0-1) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.0.2-5_amd64.deb ...
+Unpacking man-db (2.7.0.2-5) ...
+Selecting previously unselected package bash-completion.
+Preparing to unpack .../bash-completion_1%3a2.1-4.1_all.deb ...
+Unpacking bash-completion (1:2.1-4.1) ...
+Selecting previously unselected package libasprintf0c2:amd64.
+Preparing to unpack .../libasprintf0c2_0.19.4-1_amd64.deb ...
+Unpacking libasprintf0c2:amd64 (0.19.4-1) ...
+Selecting previously unselected package libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.22+15-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.22+15-2) ...
+Selecting previously unselected package libicu52:amd64.
+Preparing to unpack .../libicu52_52.1-9_amd64.deb ...
+Unpacking libicu52:amd64 (52.1-9) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.2+dfsg1-3_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.2+dfsg1-3) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ...
+Unpacking libffi6:amd64 (3.1-2+b2) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Preparing to unpack .../libglib2.0-0_2.44.1-1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.44.1-1) ...
+Selecting previously unselected package libcroco3:amd64.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ...
+Unpacking file (1:5.22+15-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.4-1_amd64.deb ...
+Unpacking gettext-base (0.19.4-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.4-1_amd64.deb ...
+Unpacking gettext (0.19.4-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.2_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.2) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150507_all.deb ...
+Unpacking debhelper (9.20150507) ...
+Selecting previously unselected package libhts1:amd64.
+Preparing to unpack .../libhts1_1.2.1-1_amd64.deb ...
+Unpacking libhts1:amd64 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:amd64.
+Preparing to unpack .../libhts-dev_1.2.1-1_amd64.deb ...
+Unpacking libhts-dev:amd64 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:amd64.
+Preparing to unpack .../libtinfo-dev_5.9+20150516-2_amd64.deb ...
+Unpacking libtinfo-dev:amd64 (5.9+20150516-2) ...
+Selecting previously unselected package libncurses5-dev:amd64.
+Preparing to unpack .../libncurses5-dev_5.9+20150516-2_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (5.9+20150516-2) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_amd64.deb ...
+Unpacking tabix (1.2.1-1) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up libpipeline1:amd64 (1.4.0-1) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+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 man-db (2.7.0.2-5) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up bash-completion (1:2.1-4.1) ...
+Setting up libasprintf0c2:amd64 (0.19.4-1) ...
+Setting up libmagic1:amd64 (1:5.22+15-2) ...
+Setting up libicu52:amd64 (52.1-9) ...
+Setting up libxml2:amd64 (2.9.2+dfsg1-3) ...
+Setting up libffi6:amd64 (3.1-2+b2) ...
+Setting up libglib2.0-0:amd64 (2.44.1-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:amd64 (0.6.8-3+b1) ...
+Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
+Setting up file (1:5.22+15-2) ...
+Setting up gettext-base (0.19.4-1) ...
+Setting up gettext (0.19.4-1) ...
+Setting up intltool-debian (0.35.0+20060710.2) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150507) ...
+Setting up libhts1:amd64 (1.2.1-1) ...
+Setting up libhts-dev:amd64 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:amd64 (5.9+20150516-2) ...
+Setting up libncurses5-dev:amd64 (5.9+20150516-2) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16-1-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-2
-Package versions: apt_1.0.9.1 base-files_7.5 base-passwd_3.5.36 bash_4.3-9.1 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 eatmydata_26-2 fakero [...]
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25-8 dpkg-dev_1.18.1 g++-4.9_4.9.2-21 gcc-4.9_4.9.2-21 libc6-dev_2.19-18 libstdc++-4.9-dev_4.9.2-21 libstdc++6_5.1.1-10 linux-libc-dev_4.0.2-1
+Package versions: apt_1.0.9.10 base-files_9.2 base-passwd_3.5.37 bash_4.3-12 bash-completion_1:2.1-4.1 binutils_2.25-8 bsdmainutils_9.0.6 bsdutils_1:2.26.2-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:4.9.2-4 cpp-4.9_4.9.2-21 dash_0.5.7-4+b1 debconf_1.5.56 debconf-i18n_1.5.56 debfoster_2.7-2 debhelper_9.20150507 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.1 dpkg-dev_1.18.1 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 eatmydata_82-6 fakeroot_1.2 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -228,11 +255,10 @@ Package versions: apt_1.0.9.1 base-files_7.5 base-passwd_3.5.36 bash_4.3-9.1 bas
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (samtools_1.1-1.dsc)
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: extracting unsigned source package (samtools_1.2-1.dsc)
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-1.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying debian-changes
@@ -253,7 +279,7 @@ SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=unstable-amd64-sbuild-3e8fcdc5-336b-4691-bf43-e99b6e156ad7
+SCHROOT_SESSION_ID=unstable-amd64-sbuild-f5de7d7c-936b-47a6-bda9-e4ff8c4e4fc1
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -262,19 +288,19 @@ USER=charles
USERNAME=charles
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
-XDG_SESSION_ID=115
+XDG_SESSION_ID=3
XDG_VTNR=7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture amd64
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -296,7 +322,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
rm -rf debian/samtools-test/
rm -f debian/*.debhelper.log
rm -f debian/files
- find . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -304,18 +331,16 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
- dpkg-source -b samtools-1.1
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
-dpkg-source: info: using source format `3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_1.1.orig.tar.gz
+ dpkg-source -b samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using source format '3.0 (quilt)'
+dpkg-source: info: building samtools using existing ./samtools_1.2.orig.tar.gz
dpkg-source: info: local changes detected, the modified files are:
- samtools-1.1/.travis.yml
- samtools-1.1/README.md
- samtools-1.1/bam.h
- samtools-1.1/test/test.pl
-dpkg-source: info: local changes have been recorded in a new patch: samtools-1.1/debian/patches/debian-changes
-dpkg-source: info: building samtools in samtools_1.1-1.debian.tar.xz
-dpkg-source: info: building samtools in samtools_1.1-1.dsc
+ samtools-1.2/.travis.yml
+ samtools-1.2/README.md
+dpkg-source: info: local changes have been recorded in a new patch: samtools-1.2/debian/patches/debian-changes
+dpkg-source: info: building samtools in samtools_1.2-1.debian.tar.xz
+dpkg-source: info: building samtools in samtools_1.2-1.dsc
debian/rules build
dh build --parallel
dh_testdir -O--parallel
@@ -345,9 +370,8 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -374,7 +398,8 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.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 padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lcurse [...]
+ar: `u' modifier ignored since `D' is the default (see `U')
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lcurses -lm -lz
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
@@ -418,91 +443,213 @@ dh_auto_test -- \
make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/BddoP4EvN2/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/bIZ9VxwNgp/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/BddoP4EvN2/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/bIZ9VxwNgp/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/BddoP4EvN2/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/bIZ9VxwNgp/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/BddoP4EvN2/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/BddoP4EvN2/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/bIZ9VxwNgp/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/BddoP4EvN2/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/bIZ9VxwNgp/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/BddoP4EvN2/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/bIZ9VxwNgp/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/BddoP4EvN2/mpileup.bam.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/bIZ9VxwNgp/mpileup.bam.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/BddoP4EvN2/mpileup.bam.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/bIZ9VxwNgp/mpileup.bam.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/BddoP4EvN2/mpileup.cram.list -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:1050-1060 /tmp/BddoP4EvN2/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:1050-1060 /tmp/bIZ9VxwNgp/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/BddoP4EvN2/mpileup.ref.fa.gz -r17:1050-1060 /tmp/BddoP4EvN2/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:1050-1060 /tmp/bIZ9VxwNgp/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
@@ -601,80 +748,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/BddoP4EvN2/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/BddoP4EvN2/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/BddoP4EvN2/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/BddoP4EvN2/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/BddoP4EvN2/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/BddoP4EvN2/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/BddoP4EvN2/view.test067.sam -h -l Library 2 /tmp/BddoP4EvN2/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/bIZ9VxwNgp/view.test067.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/BddoP4EvN2/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/bIZ9VxwNgp/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/BddoP4EvN2/view.test069.sam -h -l Library 2 /tmp/BddoP4EvN2/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/bIZ9VxwNgp/view.test069.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/BddoP4EvN2/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/bIZ9VxwNgp/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/BddoP4EvN2/view.test071.sam -h -l Library 2 /tmp/BddoP4EvN2/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/bIZ9VxwNgp/view.test071.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/BddoP4EvN2/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/bIZ9VxwNgp/view.test006.cram
.. expected failure
@@ -1057,37 +1204,41 @@ Samtools-htslib-API: bam_get_library() not yet implemented
260: Add @SQ with -T (BAM -> CRAM) .. ok
- 261: CIGAR B-operator removal .. ok
+ 261: Make CRAM with no UR field .. ok
- 262: Big SAM -> BAM .. ok
+ 262: Decoding CRAM with no UR field via -T .. ok
- 263: Big SAM -> BAM (2 threads) .. ok
+ 263: CIGAR B-operator removal .. ok
- 264: Big SAM -> BAM (4 threads) .. ok
+ 264: Big SAM -> BAM .. ok
- 265: Big SAM -> CRAM .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
- 266: Big SAM -> CRAM (2 threads) .. ok
+ 266: Big SAM -> BAM (4 threads) .. ok
- 267: Big SAM -> CRAM (4 threads) .. ok
+ 267: Big SAM -> CRAM .. ok
- 268: Subsample 0.2 (SAM input) ............ ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
- 269: Subsample 0.5 (SAM input) ............ ok
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 270: Subsample 0.8 (SAM input) ............ ok
+ 270: Subsample 0.2 (SAM input) ............ ok
- 271: Subsample 0.2 (BAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
- 272: Subsample 0.5 (BAM input) ............ ok
+ 272: Subsample 0.8 (SAM input) ............ ok
- 273: Subsample 0.8 (BAM input) ............ ok
+ 273: Subsample 0.2 (BAM input) ............ ok
- 274: Subsample 0.2 (CRAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
- 275: Subsample 0.5 (CRAM input) ............ ok
+ 275: Subsample 0.8 (BAM input) ............ ok
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
+
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1117,6 +1268,7 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
+Unsorted mode enabled
Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
@@ -1170,28 +1322,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/BddoP4EvN2/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/bIZ9VxwNgp/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/BddoP4EvN2/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/bIZ9VxwNgp/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/BddoP4EvN2/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/bIZ9VxwNgp/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/BddoP4EvN2/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/bIZ9VxwNgp/depad.001p.bam
.. expected failure
@@ -1222,16 +1374,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 22576 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/9DPBsRA8JA
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qFPGXMuTXZ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/wud9kRQhJZ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1265,10 +1415,10 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 324
+ total .. 368
+ passed .. 336
failed .. 0
- expected failure .. 18
+ expected failure .. 32
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1326,25 +1476,25 @@ make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -O--parallel
install -d debian/samtools//usr
- cp -a debian/tmp/usr/bin debian/samtools//usr/
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
- cp -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
install -d debian/samtools-test/usr/share/samtools
- cp -a ./test debian/samtools-test/usr/share/samtools/
+ cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/
dh_installdocs -O--parallel
- install -g 0 -o 0 -d debian/samtools/usr/share/doc/samtools
- cp -a AUTHORS debian/samtools/usr/share/doc/samtools
- cp -a debian/reference debian/samtools/usr/share/doc/samtools
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
chown -R 0:0 debian/samtools/usr/share/doc
chmod -R go=rX debian/samtools/usr/share/doc
chmod -R u\+rw debian/samtools/usr/share/doc
- install -g 0 -o 0 -m 644 -p debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
- install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools/usr/share/doc/samtools/copyright
- install -g 0 -o 0 -d debian/samtools-test/usr/share/doc/samtools-test
- install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ install -d debian/samtools-test/usr/share/doc/samtools-test
+ install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
dh_installchangelogs -O--parallel
- install -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
- install -o 0 -g 0 -p -m644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
dh_installman -O--parallel
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
@@ -1367,25 +1517,25 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_fixperms -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
- find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/samtools-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/samtools-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
- find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/samtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/samtools-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
dh_strip -O--parallel
@@ -1400,43 +1550,45 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
rm -f debian/samtools/DEBIAN/shlibs
rm -f debian/samtools-test/DEBIAN/shlibs
dh_shlibdeps -O--parallel
- install -o 0 -g 0 -d debian/samtools/DEBIAN
+ install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
- install -o 0 -g 0 -d debian/samtools-test/DEBIAN
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long were not linked against libhts.so.1 (they use none of the library's symbols)
+ install -d debian/samtools-test/DEBIAN
dh_installdeb -O--parallel
dh_gencontrol -O--parallel
echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
- chmod 644 debian/samtools/DEBIAN/control
+ chmod 0644 debian/samtools/DEBIAN/control
chown 0:0 debian/samtools/DEBIAN/control
echo misc:Depends= >> debian/samtools-test.substvars
+ echo misc:Pre-Depends= >> debian/samtools-test.substvars
dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools-test: unused substitution variable ${perl:Depends}
- chmod 644 debian/samtools-test/DEBIAN/control
+ chmod 0644 debian/samtools-test/DEBIAN/control
chown 0:0 debian/samtools-test/DEBIAN/control
dh_md5sums -O--parallel
(cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
- chmod 644 debian/samtools/DEBIAN/md5sums
+ chmod 0644 debian/samtools/DEBIAN/md5sums
chown 0:0 debian/samtools/DEBIAN/md5sums
(cd debian/samtools-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
- chmod 644 debian/samtools-test/DEBIAN/md5sums
+ chmod 0644 debian/samtools-test/DEBIAN/md5sums
chown 0:0 debian/samtools-test/DEBIAN/md5sums
dh_builddeb -O--parallel
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package `samtools' in `../samtools_1.1-1_amd64.deb'.
+dpkg-deb: building package 'samtools' in '../samtools_1.2-1_amd64.deb'.
dpkg-deb --build debian/samtools-test ..
-dpkg-deb: building package `samtools-test' in `../samtools-test_1.1-1_all.deb'.
- dpkg-genchanges >../samtools_1.1-1_amd64.changes
+dpkg-deb: building package 'samtools-test' in '../samtools-test_1.2-1_all.deb'.
+ dpkg-genchanges >../samtools_1.2-1_amd64.changes
dpkg-genchanges: including full source code in upload
- dpkg-source --after-build samtools-1.1
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: full upload (original source is included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0908
+Build finished at 20150616-0617
Finished
────────
@@ -1453,8 +1605,13 @@ lintian
Merged Build-Depends: lintian
Filtered Build-Depends: lintian
-dpkg-deb: building package `sbuild-build-depends-lintian-dummy' in `/«BUILDDIR»/resolver-jRfKH3/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/«BUILDDIR»/resolver-MYREbF/apt_archive/sbuild-build-depends-lintian-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1468,169 +1625,173 @@ Reading state information...
The following extra packages will be installed:
diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
- libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
+ libexporter-tiny-perl libfile-basedir-perl libio-socket-inet6-perl
libio-socket-ssl-perl libio-string-perl libipc-run-perl
- liblist-moreutils-perl libmailtools-perl libnet-dns-perl
- libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
+ libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl
+ libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
- libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
- patchutils t1utils
+ libsub-name-perl libtext-levenshtein-perl lintian netbase patchutils t1utils
Suggested packages:
- ca-certificates libhtml-parser-perl libhtml-template-perl libxml-simple-perl
- libwww-perl binutils-multiarch libyaml-perl
+ ca-certificates libhtml-template-perl libxml-simple-perl binutils-multiarch
+ libyaml-perl
Recommended packages:
libauthen-sasl-perl libperlio-gzip-perl ifupdown
The following NEW packages will be installed:
diffstat hardening-includes libapt-pkg-perl libarchive-zip-perl
libclass-accessor-perl libclone-perl libdigest-hmac-perl libemail-valid-perl
- libfile-basedir-perl libio-pty-perl libio-socket-inet6-perl
+ libexporter-tiny-perl libfile-basedir-perl libio-socket-inet6-perl
libio-socket-ssl-perl libio-string-perl libipc-run-perl
- liblist-moreutils-perl libmailtools-perl libnet-dns-perl
- libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
+ libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl
+ libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
libnet-ssleay-perl libparse-debianchangelog-perl libsocket6-perl libssl1.0.0
- libsub-name-perl libtext-levenshtein-perl liburi-perl lintian netbase
- patchutils sbuild-build-depends-lintian-dummy t1utils
-debconf: delaying package configuration, since apt-utils is not installed
+ libsub-name-perl libtext-levenshtein-perl lintian netbase patchutils
+ sbuild-build-depends-lintian-dummy t1utils
0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/3597 kB of archives.
-After this operation, 12.0 MB of additional disk space will be used.
-Selecting previously unselected package libssl1.0.0:amd64.
-(Reading database ... 13304 files and directories currently installed.)
-Preparing to unpack .../libssl1.0.0_1.0.1i-2_amd64.deb ...
-Unpacking libssl1.0.0:amd64 (1.0.1i-2) ...
-Selecting previously unselected package netbase.
-Preparing to unpack .../archives/netbase_5.2_all.deb ...
-Unpacking netbase (5.2) ...
-Selecting previously unselected package diffstat.
-Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
-Unpacking diffstat (1.58-1) ...
-Selecting previously unselected package hardening-includes.
-Preparing to unpack .../hardening-includes_2.5+nmu1_all.deb ...
-Unpacking hardening-includes (2.5+nmu1) ...
-Selecting previously unselected package libapt-pkg-perl.
-Preparing to unpack .../libapt-pkg-perl_0.1.29+b2_amd64.deb ...
-Unpacking libapt-pkg-perl (0.1.29+b2) ...
-Selecting previously unselected package libarchive-zip-perl.
-Preparing to unpack .../libarchive-zip-perl_1.38-1_all.deb ...
-Unpacking libarchive-zip-perl (1.38-1) ...
-Selecting previously unselected package libsub-name-perl.
-Preparing to unpack .../libsub-name-perl_0.07-1+b1_amd64.deb ...
-Unpacking libsub-name-perl (0.07-1+b1) ...
-Selecting previously unselected package libclass-accessor-perl.
-Preparing to unpack .../libclass-accessor-perl_0.34-1_all.deb ...
-Unpacking libclass-accessor-perl (0.34-1) ...
-Selecting previously unselected package libclone-perl.
-Preparing to unpack .../libclone-perl_0.37-1+b1_amd64.deb ...
-Unpacking libclone-perl (0.37-1+b1) ...
-Selecting previously unselected package libdigest-hmac-perl.
-Preparing to unpack .../libdigest-hmac-perl_1.03+dfsg-1_all.deb ...
-Unpacking libdigest-hmac-perl (1.03+dfsg-1) ...
-Selecting previously unselected package libnet-ssleay-perl.
-Preparing to unpack .../libnet-ssleay-perl_1.65-1+b1_amd64.deb ...
-Unpacking libnet-ssleay-perl (1.65-1+b1) ...
-Selecting previously unselected package libio-socket-ssl-perl.
-Preparing to unpack .../libio-socket-ssl-perl_1.998-1_all.deb ...
-Unpacking libio-socket-ssl-perl (1.998-1) ...
-Selecting previously unselected package libnet-smtp-ssl-perl.
-Preparing to unpack .../libnet-smtp-ssl-perl_1.01-3_all.deb ...
-Unpacking libnet-smtp-ssl-perl (1.01-3) ...
-Selecting previously unselected package libmailtools-perl.
-Preparing to unpack .../libmailtools-perl_2.13-1_all.deb ...
-Unpacking libmailtools-perl (2.13-1) ...
-Selecting previously unselected package libsocket6-perl.
-Preparing to unpack .../libsocket6-perl_0.25-1+b1_amd64.deb ...
-Unpacking libsocket6-perl (0.25-1+b1) ...
-Selecting previously unselected package libio-socket-inet6-perl.
-Preparing to unpack .../libio-socket-inet6-perl_2.72-1_all.deb ...
-Unpacking libio-socket-inet6-perl (2.72-1) ...
-Selecting previously unselected package libnet-ip-perl.
-Preparing to unpack .../libnet-ip-perl_1.26-1_all.deb ...
-Unpacking libnet-ip-perl (1.26-1) ...
-Selecting previously unselected package libnet-dns-perl.
-Preparing to unpack .../libnet-dns-perl_0.79-2_amd64.deb ...
-Unpacking libnet-dns-perl (0.79-2) ...
-Selecting previously unselected package libnet-domain-tld-perl.
-Preparing to unpack .../libnet-domain-tld-perl_1.72-1_all.deb ...
-Unpacking libnet-domain-tld-perl (1.72-1) ...
-Selecting previously unselected package libemail-valid-perl.
-Preparing to unpack .../libemail-valid-perl_1.195-1_all.deb ...
-Unpacking libemail-valid-perl (1.195-1) ...
-Selecting previously unselected package libfile-basedir-perl.
-Preparing to unpack .../libfile-basedir-perl_0.03-1_all.deb ...
-Unpacking libfile-basedir-perl (0.03-1) ...
-Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
-Selecting previously unselected package libio-string-perl.
-Preparing to unpack .../libio-string-perl_1.08-3_all.deb ...
-Unpacking libio-string-perl (1.08-3) ...
-Selecting previously unselected package libipc-run-perl.
-Preparing to unpack .../libipc-run-perl_0.92-1_all.deb ...
-Unpacking libipc-run-perl (0.92-1) ...
-Selecting previously unselected package liblist-moreutils-perl.
-Preparing to unpack .../liblist-moreutils-perl_0.33-2+b1_amd64.deb ...
-Unpacking liblist-moreutils-perl (0.33-2+b1) ...
-Selecting previously unselected package libparse-debianchangelog-perl.
-Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-1.1_all.deb ...
-Unpacking libparse-debianchangelog-perl (1.2.0-1.1) ...
-Selecting previously unselected package libtext-levenshtein-perl.
-Preparing to unpack .../libtext-levenshtein-perl_0.09-1_all.deb ...
-Unpacking libtext-levenshtein-perl (0.09-1) ...
-Selecting previously unselected package liburi-perl.
-Preparing to unpack .../liburi-perl_1.64-1_all.deb ...
-Unpacking liburi-perl (1.64-1) ...
-Selecting previously unselected package patchutils.
-Preparing to unpack .../patchutils_0.3.3-1_amd64.deb ...
-Unpacking patchutils (0.3.3-1) ...
-Selecting previously unselected package t1utils.
-Preparing to unpack .../t1utils_1.37-2.1_amd64.deb ...
-Unpacking t1utils (1.37-2.1) ...
-Selecting previously unselected package lintian.
-Preparing to unpack .../lintian_2.5.27_all.deb ...
-Unpacking lintian (2.5.27) ...
-Selecting previously unselected package sbuild-build-depends-lintian-dummy.
-Preparing to unpack .../sbuild-build-depends-lintian-dummy.deb ...
-Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
-Processing triggers for man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up libssl1.0.0:amd64 (1.0.1i-2) ...
-Setting up netbase (5.2) ...
-Setting up diffstat (1.58-1) ...
-Setting up hardening-includes (2.5+nmu1) ...
-Setting up libapt-pkg-perl (0.1.29+b2) ...
-Setting up libarchive-zip-perl (1.38-1) ...
-Setting up libsub-name-perl (0.07-1+b1) ...
-Setting up libclass-accessor-perl (0.34-1) ...
-Setting up libclone-perl (0.37-1+b1) ...
-Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
-Setting up libnet-ssleay-perl (1.65-1+b1) ...
-Setting up libio-socket-ssl-perl (1.998-1) ...
-Setting up libnet-smtp-ssl-perl (1.01-3) ...
-Setting up libmailtools-perl (2.13-1) ...
-Setting up libsocket6-perl (0.25-1+b1) ...
-Setting up libio-socket-inet6-perl (2.72-1) ...
-Setting up libnet-ip-perl (1.26-1) ...
-Setting up libnet-dns-perl (0.79-2) ...
-Setting up libnet-domain-tld-perl (1.72-1) ...
-Setting up libemail-valid-perl (1.195-1) ...
-Setting up libfile-basedir-perl (0.03-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libio-string-perl (1.08-3) ...
-Setting up libipc-run-perl (0.92-1) ...
-Setting up liblist-moreutils-perl (0.33-2+b1) ...
-Setting up libparse-debianchangelog-perl (1.2.0-1.1) ...
-Setting up libtext-levenshtein-perl (0.09-1) ...
-Setting up liburi-perl (1.64-1) ...
-Setting up patchutils (0.3.3-1) ...
-Setting up t1utils (1.37-2.1) ...
-Setting up lintian (2.5.27) ...
-Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Need to get 1376 kB/3884 kB of archives.
+After this operation, 12.5 MB of additional disk space will be used.
+Get:1 http://ftp.jp.debian.org/debian/ unstable/main libssl1.0.0 amd64 1.0.2c-1 [1273 kB]
+Get:2 http://ftp.jp.debian.org/debian/ unstable/main libipc-system-simple-perl all 1.25-2 [26.7 kB]
+Get:3 http://ftp.jp.debian.org/debian/ unstable/main libfile-basedir-perl all 0.07-1 [17.5 kB]
+Get:4 http://ftp.jp.debian.org/debian/ unstable/main libparse-debianchangelog-perl all 1.2.0-4 [58.9 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 1376 kB in 3s (360 kB/s)
+Selecting previously unselected package libssl1.0.0:amd64.
+(Reading database ...
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(Reading database ... 13712 files and directories currently installed.)
+Preparing to unpack .../libssl1.0.0_1.0.2c-1_amd64.deb ...
+Unpacking libssl1.0.0:amd64 (1.0.2c-1) ...
+Selecting previously unselected package netbase.
+Preparing to unpack .../archives/netbase_5.3_all.deb ...
+Unpacking netbase (5.3) ...
+Selecting previously unselected package diffstat.
+Preparing to unpack .../diffstat_1.58-1_amd64.deb ...
+Unpacking diffstat (1.58-1) ...
+Selecting previously unselected package hardening-includes.
+Preparing to unpack .../hardening-includes_2.7_all.deb ...
+Unpacking hardening-includes (2.7) ...
+Selecting previously unselected package libapt-pkg-perl.
+Preparing to unpack .../libapt-pkg-perl_0.1.29+b2_amd64.deb ...
+Unpacking libapt-pkg-perl (0.1.29+b2) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.39-1_all.deb ...
+Unpacking libarchive-zip-perl (1.39-1) ...
+Selecting previously unselected package libsub-name-perl.
+Preparing to unpack .../libsub-name-perl_0.12-1_amd64.deb ...
+Unpacking libsub-name-perl (0.12-1) ...
+Selecting previously unselected package libclass-accessor-perl.
+Preparing to unpack .../libclass-accessor-perl_0.34-1_all.deb ...
+Unpacking libclass-accessor-perl (0.34-1) ...
+Selecting previously unselected package libclone-perl.
+Preparing to unpack .../libclone-perl_0.38-1_amd64.deb ...
+Unpacking libclone-perl (0.38-1) ...
+Selecting previously unselected package libdigest-hmac-perl.
+Preparing to unpack .../libdigest-hmac-perl_1.03+dfsg-1_all.deb ...
+Unpacking libdigest-hmac-perl (1.03+dfsg-1) ...
+Selecting previously unselected package libnet-ssleay-perl.
+Preparing to unpack .../libnet-ssleay-perl_1.68-1_amd64.deb ...
+Unpacking libnet-ssleay-perl (1.68-1) ...
+Selecting previously unselected package libio-socket-ssl-perl.
+Preparing to unpack .../libio-socket-ssl-perl_2.016-1_all.deb ...
+Unpacking libio-socket-ssl-perl (2.016-1) ...
+Selecting previously unselected package libnet-smtp-ssl-perl.
+Preparing to unpack .../libnet-smtp-ssl-perl_1.01-3_all.deb ...
+Unpacking libnet-smtp-ssl-perl (1.01-3) ...
+Selecting previously unselected package libmailtools-perl.
+Preparing to unpack .../libmailtools-perl_2.13-1_all.deb ...
+Unpacking libmailtools-perl (2.13-1) ...
+Selecting previously unselected package libsocket6-perl.
+Preparing to unpack .../libsocket6-perl_0.25-1+b1_amd64.deb ...
+Unpacking libsocket6-perl (0.25-1+b1) ...
+Selecting previously unselected package libio-socket-inet6-perl.
+Preparing to unpack .../libio-socket-inet6-perl_2.72-2_all.deb ...
+Unpacking libio-socket-inet6-perl (2.72-2) ...
+Selecting previously unselected package libnet-ip-perl.
+Preparing to unpack .../libnet-ip-perl_1.26-1_all.deb ...
+Unpacking libnet-ip-perl (1.26-1) ...
+Selecting previously unselected package libnet-dns-perl.
+Preparing to unpack .../libnet-dns-perl_0.81-2_amd64.deb ...
+Unpacking libnet-dns-perl (0.81-2) ...
+Selecting previously unselected package libnet-domain-tld-perl.
+Preparing to unpack .../libnet-domain-tld-perl_1.73-1_all.deb ...
+Unpacking libnet-domain-tld-perl (1.73-1) ...
+Selecting previously unselected package libemail-valid-perl.
+Preparing to unpack .../libemail-valid-perl_1.195-1_all.deb ...
+Unpacking libemail-valid-perl (1.195-1) ...
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+Unpacking libexporter-tiny-perl (0.042-1) ...
+Selecting previously unselected package libipc-system-simple-perl.
+Preparing to unpack .../libipc-system-simple-perl_1.25-2_all.deb ...
+Unpacking libipc-system-simple-perl (1.25-2) ...
+Selecting previously unselected package libfile-basedir-perl.
+Preparing to unpack .../libfile-basedir-perl_0.07-1_all.deb ...
+Unpacking libfile-basedir-perl (0.07-1) ...
+Selecting previously unselected package libio-string-perl.
+Preparing to unpack .../libio-string-perl_1.08-3_all.deb ...
+Unpacking libio-string-perl (1.08-3) ...
+Selecting previously unselected package libipc-run-perl.
+Preparing to unpack .../libipc-run-perl_0.94-1_all.deb ...
+Unpacking libipc-run-perl (0.94-1) ...
+Selecting previously unselected package liblist-moreutils-perl.
+Preparing to unpack .../liblist-moreutils-perl_0.410-1_amd64.deb ...
+Unpacking liblist-moreutils-perl (0.410-1) ...
+Selecting previously unselected package libparse-debianchangelog-perl.
+Preparing to unpack .../libparse-debianchangelog-perl_1.2.0-4_all.deb ...
+Unpacking libparse-debianchangelog-perl (1.2.0-4) ...
+Selecting previously unselected package libtext-levenshtein-perl.
+Preparing to unpack .../libtext-levenshtein-perl_0.12-1_all.deb ...
+Unpacking libtext-levenshtein-perl (0.12-1) ...
+Selecting previously unselected package patchutils.
+Preparing to unpack .../patchutils_0.3.4-1_amd64.deb ...
+Unpacking patchutils (0.3.4-1) ...
+Selecting previously unselected package t1utils.
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+Unpacking t1utils (1.38-4) ...
+Selecting previously unselected package lintian.
+Preparing to unpack .../lintian_2.5.31_all.deb ...
+Unpacking lintian (2.5.31) ...
+Selecting previously unselected package sbuild-build-depends-lintian-dummy.
+Preparing to unpack .../sbuild-build-depends-lintian-dummy.deb ...
+Unpacking sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for man-db (2.7.0.2-5) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libssl1.0.0:amd64 (1.0.2c-1) ...
+Setting up netbase (5.3) ...
+Setting up diffstat (1.58-1) ...
+Setting up hardening-includes (2.7) ...
+Setting up libapt-pkg-perl (0.1.29+b2) ...
+Setting up libarchive-zip-perl (1.39-1) ...
+Setting up libsub-name-perl (0.12-1) ...
+Setting up libclass-accessor-perl (0.34-1) ...
+Setting up libclone-perl (0.38-1) ...
+Setting up libdigest-hmac-perl (1.03+dfsg-1) ...
+Setting up libnet-ssleay-perl (1.68-1) ...
+Setting up libio-socket-ssl-perl (2.016-1) ...
+Setting up libnet-smtp-ssl-perl (1.01-3) ...
+Setting up libmailtools-perl (2.13-1) ...
+Setting up libsocket6-perl (0.25-1+b1) ...
+Setting up libio-socket-inet6-perl (2.72-2) ...
+Setting up libnet-ip-perl (1.26-1) ...
+Setting up libnet-dns-perl (0.81-2) ...
+Setting up libnet-domain-tld-perl (1.73-1) ...
+Setting up libemail-valid-perl (1.195-1) ...
+Setting up libexporter-tiny-perl (0.042-1) ...
+Setting up libipc-system-simple-perl (1.25-2) ...
+Setting up libfile-basedir-perl (0.07-1) ...
+Setting up libio-string-perl (1.08-3) ...
+Setting up libipc-run-perl (0.94-1) ...
+Setting up liblist-moreutils-perl (0.410-1) ...
+Setting up libparse-debianchangelog-perl (1.2.0-4) ...
+Setting up libtext-levenshtein-perl (0.12-1) ...
+Setting up patchutils (0.3.4-1) ...
+Setting up t1utils (1.38-4) ...
+Setting up lintian (2.5.31) ...
+Setting up sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-18) ...
I: samtools source: quilt-patch-using-template-description debian-changes
-W: samtools source: newer-standards-version 3.9.6 (current is 3.9.5)
P: samtools source: debian-watch-may-check-gpg-signature
P: samtools-test: no-upstream-changelog
I: samtools-test: description-synopsis-might-not-be-phrased-properly
+I: samtools: spelling-error-in-binary usr/bin/samtools compres compress
P: samtools: no-upstream-changelog
W: samtools: script-with-language-extension usr/bin/blast2sam.pl
W: samtools: script-with-language-extension usr/bin/bowtie2sam.pl
@@ -1685,15 +1846,15 @@ I: Lintian run was successful.
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.1-1_amd64.changes:
+samtools_1.2-1_amd64.changes:
─────────────────────────────
Format: 1.8
-Date: Thu, 25 Sep 2014 09:04:20 +0900
+Date: Tue, 16 Jun 2015 06:12:12 +0900
Source: samtools
Binary: samtools samtools-test
-Architecture: source amd64 all
-Version: 1.1-1
+Architecture: source all amd64
+Version: 1.2-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -1702,51 +1863,308 @@ Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package.
Changes:
- samtools (1.1-1) unstable; urgency=medium
+ samtools (1.2-1) unstable; urgency=medium
.
- c448d48 Merge tag '1.1' into debian/unstable
- d12ab1e Merge branch 'develop' into debian/unstable to solve issue
- with regression tests needing a pseudo-terminal.
- See https://github.com/samtools/samtools/issues/300
- c87f8ce Add autopkg tests.
- 7c50b7b Removed python-wrong-path-for-interpreter.patch
- (issue solved upstream).
+ a5f28a0 Merge tag '1.2' into debian/unstable
+ c542e84 Build-depend on libhts-dev 1.2.
+ 6c2d9cd Build-depend and recommend libio-pty-perl.
+ (Needed for the regression tests.)
+ 23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option.
+ 1091aab Refreshed fuzzy patches.
Checksums-Sha1:
- f58cc8cdc87a5fe44cae59e10c47ff48c9b0225f 1235 samtools_1.1-1.dsc
- ca446ec24eabd2f71605dde55a787f182cb50f13 4320951 samtools_1.1.orig.tar.gz
- 0e4de8be00fb4dd375048b1b1dc05e2f120e2ead 10164 samtools_1.1-1.debian.tar.xz
- 3424183e6577c856a09f4f838c1a398c8e5744ba 378168 samtools_1.1-1_amd64.deb
- f2542cc1d07aef31d216d43630c87c9edf38cabd 2644466 samtools-test_1.1-1_all.deb
+ 08ea4f543ece1659a28623f439098622561070ec 1248 samtools_1.2-1.dsc
+ 9fabb4903b9d1521aeea8a5538e64aefe8e85526 4318615 samtools_1.2.orig.tar.gz
+ a91e9483810ed9ed0e979138febf467b6db6956d 9596 samtools_1.2-1.debian.tar.xz
+ 5af2830490b1588c6e2bcd3021733c0681cddfb4 2644688 samtools-test_1.2-1_all.deb
+ 5d97f7b4d27954e75904cd4a6155422f65022e57 392492 samtools_1.2-1_amd64.deb
Checksums-Sha256:
- 51d2a985b0ac982d983f5766c2287081186e2f89e3fdbd9c5e0f02b07ae4790a 1235 samtools_1.1-1.dsc
- cee231e33b7290be8e07dea43a99b885d9df79d957625ac84879b47ff91cda69 4320951 samtools_1.1.orig.tar.gz
- 50e5d2299c2d99ce53647fc0cb08eee53bc31d08bfa7d7cc981e6fae28ab231b 10164 samtools_1.1-1.debian.tar.xz
- 55ca7fb40430ba8c17967568f5c48ee19379bdbae3cb218456dae7fed5ea107d 378168 samtools_1.1-1_amd64.deb
- 5fb20f9d61452c8863e6ff42d2ea0d9ec72211fb9dd43cca3b55eeeb49985196 2644466 samtools-test_1.1-1_all.deb
+ ab7f8b120ba2abc420c04197fc70b7b6e6d501cc063feaa96c309427f7936dac 1248 samtools_1.2-1.dsc
+ e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47 4318615 samtools_1.2.orig.tar.gz
+ c3a6bead979cd8bb0b8fec3e9d6b2bb352db21ae4fdac8ad214757aed72bad23 9596 samtools_1.2-1.debian.tar.xz
+ 5a3017e37793e4dc1daa7f8c029cb943d98001cd580d110bf569093b0bbb7e2d 2644688 samtools-test_1.2-1_all.deb
+ 5af217333dd6c66de5667be1c7a3edb695f370a5add22458081747a7b8968856 392492 samtools_1.2-1_amd64.deb
Files:
- 1d7d68a126fe90d8366eb3fed809230c 378168 science optional samtools_1.1-1_amd64.deb
- 9ffe69f7310c265243d2fd553c322435 2644466 science optional samtools-test_1.1-1_all.deb
- 55da7a41c3b167afed4063667eaed949 1235 science optional samtools_1.1-1.dsc
- 5fda5c175d04bff39c56078aea7cd3b1 4320951 science optional samtools_1.1.orig.tar.gz
- 40b3a1f31e22323c8d247e1bff1a9c52 10164 science optional samtools_1.1-1.debian.tar.xz
+ 391c4f642dbc7d9c48cadc02d924644b 1248 science optional samtools_1.2-1.dsc
+ 2748356ef392c0694ca1142de37cf2aa 4318615 science optional samtools_1.2.orig.tar.gz
+ af3dbbae0acff0b7f989b54455839b56 9596 science optional samtools_1.2-1.debian.tar.xz
+ 31a29a2c1ccf9235d4967d0582e25b51 2644688 science optional samtools-test_1.2-1_all.deb
+ d7ce058d6c3b4d64fc6530615c960f6e 392492 science optional samtools_1.2-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.1-1_amd64.deb
+samtools-test_1.2-1_all.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 2644688 bytes: control archive=5620 bytes.
+ 494 bytes, 15 lines control
+ 17627 bytes, 215 lines md5sums
+ Package: samtools-test
+ Source: samtools
+ Version: 1.2-1
+ Architecture: all
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 9222
+ Recommends: libio-pty-perl
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: test files for the samtools package.
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format.
+ .
+ This package contains test files for the samtools package.
+
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/doc/samtools-test/
+-rw-r--r-- root/root 3392 2015-06-16 06:12 ./usr/share/doc/samtools-test/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-06-15 21:30 ./usr/share/doc/samtools-test/copyright
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/
+-rw-r--r-- root/root 5280 2015-02-03 00:18 ./usr/share/samtools/test/dat/bam2fq.001.sam
+-rw-r--r-- root/root 1292 2015-02-03 00:18 ./usr/share/samtools/test/dat/cat.hdr
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/
+-rw-r--r-- root/root 57 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
+-rw-r--r-- root/root 61 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
+-rw-r--r-- root/root 36 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
+-rw-r--r-- root/root 31 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
+-rw-r--r-- root/root 42 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001.fa
+-rw-r--r-- root/root 16 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001.fa.fai
+-rw-r--r-- root/root 7908 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001p.sam
+-rw-r--r-- root/root 7914 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001u.sam
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/empty.expected
+-rw-r--r-- root/root 624 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom.out
+-rw-r--r-- root/root 5090 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom.sam
+-rw-r--r-- root/root 92 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom_bai_index.err
+-rw-r--r-- root/root 351091 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.1.sam
+-rw-r--r-- root/root 104866 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.2.sam
+-rw-r--r-- root/root 105843 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.3.sam
+-rw-r--r-- root/root 78 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.err.1
+-rw-r--r-- root/root 2716 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.1
+-rw-r--r-- root/root 81484 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.2
+-rw-r--r-- root/root 295 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.3
+-rw-r--r-- root/root 113722 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.4
+-rw-r--r-- root/root 4284 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.ref.fa
+-rw-r--r-- root/root 17 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai
+-rw-r--r-- root/root 758 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.bam
+-rw-r--r-- root/root 264 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai
+-rw-r--r-- root/root 1429 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.sam
+-rw-r--r-- root/root 687 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.bam
+-rw-r--r-- root/root 192 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.bam.bai
+-rw-r--r-- root/root 1252 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.sam
+-rw-r--r-- root/root 655 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.bam
+-rw-r--r-- root/root 176 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.bam.bai
+-rw-r--r-- root/root 1253 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.sam
+-rw-r--r-- root/root 1335 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.01.bed
+-rw-r--r-- root/root 1134 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.02.bed
+-rw-r--r-- root/root 130 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.fa
+-rw-r--r-- root/root 33 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.fa.fai
+-rw-r--r-- root/root 5073 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.sam
+-rw-r--r-- root/root 1313 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.01.bed
+-rw-r--r-- root/root 1302 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.02.bed
+-rw-r--r-- root/root 64 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.fa
+-rw-r--r-- root/root 13 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.fa.fai
+-rw-r--r-- root/root 3692 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.sam
+-rw-r--r-- root/root 2142 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.003.expected.sam
+-rw-r--r-- root/root 2224 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.003.sam
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/
+-rw-r--r-- root/root 894 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected
+-rw-r--r-- root/root 82 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err
+-rw-r--r-- root/root 1047 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam
+-rw-r--r-- root/root 1102 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected
+-rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam
+-rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected
+-rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam
+-rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected
+-rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/5_ct.sam
+-rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/5_ct.sam.expected
+-rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/6_ct_replace.sam
+-rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/
+-rw-r--r-- root/root 58 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/merge/
+-rw-r--r-- root/root 1181 2015-02-03 00:18 ./usr/share/samtools/test/merge/2.merge.expected.bam
+-rw-r--r-- root/root 1199 2015-02-03 00:18 ./usr/share/samtools/test/merge/3.merge.expected.bam
+-rw-r--r-- root/root 525 2015-02-03 00:18 ./usr/share/samtools/test/merge/3.merge.expected.err
+-rw-r--r-- root/root 46 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_3.fofn
+-rw-r--r-- root/root 15673 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_bam_translate.c
+-rw-r--r-- root/root 184 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_header.sam
+-rw-r--r-- root/root 2482 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_pretty_header.c
+-rw-r--r-- root/root 3531 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_rtrans_build.c
+-rw-r--r-- root/root 15077 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_trans_tbl_init.c
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/mpileup/
+-rw-r--r-- root/root 525 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/1read.bam
+-rw-r--r-- root/root 5 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/1read.sam
+-rw-r--r-- root/root 1886 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/anomalous.sam
+-rw-r--r-- root/root 293 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#ID.bam
+-rw-r--r-- root/root 377 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#ID2.bam
+-rw-r--r-- root/root 265 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#clip.bam
+-rw-r--r-- root/root 299 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad1.bam
+-rw-r--r-- root/root 349 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad2.bam
+-rw-r--r-- root/root 382 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad3.bam
+-rw-r--r-- root/root 29 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1.fa
+-rw-r--r-- root/root 26 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1.fa.fai
+-rw-r--r-- root/root 557 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.bam
+-rw-r--r-- root/root 416 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.bam.bai
+-rw-r--r-- root/root 13183 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.cram
+-rw-r--r-- root/root 75 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.cram.crai
+-rw-r--r-- root/root 2033 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.sam
+-rw-r--r-- root/root 345315 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#large_seq.bam
+-rw-r--r-- root/root 233 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap.bam
+-rw-r--r-- root/root 896 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap1.bam
+-rw-r--r-- root/root 1344 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap2.bam
+-rw-r--r-- root/root 1060702 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce.fa
+-rw-r--r-- root/root 230 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce.fa.fai
+-rw-r--r-- root/root 252022 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/deep.sam
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/mpileup/expected/
+-rw-r--r-- root/root 1336220 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/1.out.xz
+-rw-r--r-- root/root 607 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/10.out
+-rw-r--r-- root/root 238 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/11.out
+-rw-r--r-- root/root 306 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/12.out
+-rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/13.out
+-rw-r--r-- root/root 282158 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/14.out
+-rw-r--r-- root/root 282158 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/15.out
+-rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/16.out
+-rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/17.out
+-rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/18.out
+-rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/19.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/2.out
+-rw-r--r-- root/root 58067 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/20.out
+-rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/21.out
+-rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/22.out
+-rw-r--r-- root/root 2252 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/23.out
+-rw-r--r-- root/root 2352 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/24.out
+-rw-r--r-- root/root 2352 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/25.out
+-rw-r--r-- root/root 1706 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/26.out
+-rw-r--r-- root/root 2112 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/27.out
+-rw-r--r-- root/root 165459 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/28.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/29.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/3.out
+-rw-r--r-- root/root 1501 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/30.out
+-rw-r--r-- root/root 1503 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/31.out
+-rw-r--r-- root/root 1501 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/32.out
+-rw-r--r-- root/root 176 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/33.out
+-rw-r--r-- root/root 176 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/34.out
+-rw-r--r-- root/root 59199 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/35.out
+-rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/37.out
+-rw-r--r-- root/root 2882 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/38.out
+-rw-r--r-- root/root 475 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/39.out
+-rw-r--r-- root/root 4352 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/4.out
+-rw-r--r-- root/root 2155 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/40.out
+-rw-r--r-- root/root 559 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/41.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/42.out
+-rw-r--r-- root/root 103144 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/43.out
+-rw-r--r-- root/root 103144 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/44.out
+-rw-r--r-- root/root 111941 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/45.out
+-rw-r--r-- root/root 111941 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/46.out
+-rw-r--r-- root/root 5 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/47.out
+-rw-r--r-- root/root 384139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/48.out
+-rw-r--r-- root/root 384139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/49.out
+-rw-r--r-- root/root 244 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/5.out
+-rw-r--r-- root/root 428319 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/50.out
+-rw-r--r-- root/root 404654 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/51.out
+-rw-r--r-- root/root 37 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/52.out
+-rw-r--r-- root/root 138 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/53.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/54.out
+-rw-r--r-- root/root 139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/55.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/56.out
+-rw-r--r-- root/root 139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/57.out
+-rw-r--r-- root/root 138 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/58.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/59.out
+-rw-r--r-- root/root 362 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/6.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/60.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/61.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/62.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/63.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/64.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/65.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/66.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/67.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/68.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/69.out
+-rw-r--r-- root/root 458 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/7.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/70.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/71.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/72.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/73.out
+-rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/74.out
+-rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/75.out
+-rw-r--r-- root/root 221725 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/76.out
+-rw-r--r-- root/root 318473 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/77.out
+-rw-r--r-- root/root 204 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/8.out
+-rw-r--r-- root/root 137 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/9.out
+-rw-r--r-- root/root 1561 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/indels.sam
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/
+-rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
+-rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
+-rw-r--r-- root/root 4200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
+-rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
+-rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
+-rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
+-rw-r--r-- root/root 280 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup-E.bam
+-rw-r--r-- root/root 71637 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.1.bam
+-rw-r--r-- root/root 776 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.1.bam.bai
+-rw-r--r-- root/root 31556 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.2.bam
+-rw-r--r-- root/root 31216 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.3.bam
+-rw-r--r-- root/root 4284 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.ref.fa
+-rw-r--r-- root/root 17 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.ref.fa.fai
+-rw-r--r-- root/root 7616 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.reg
+-rw-r--r-- root/root 793 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/overlap50.sam
+-rw-r--r-- root/root 583 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/overlapIllumina.bam
+-rw-r--r-- root/root 250 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/regions
+-rwxr-xr-x root/root 4687 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/regression.sh
+-rw-r--r-- root/root 215 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx#minimal.bam
+-rw-r--r-- root/root 247 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx#triplet.bam
+-rw-r--r-- root/root 56 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx.fa
+-rw-r--r-- root/root 29 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx.fa.fai
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/split/
+-rw-r--r-- root/root 3597 2015-02-03 00:18 ./usr/share/samtools/test/split/test_count_rg.c
+-rw-r--r-- root/root 3951 2015-02-03 00:18 ./usr/share/samtools/test/split/test_expand_format_string.c
+-rw-r--r-- root/root 5173 2015-02-03 00:18 ./usr/share/samtools/test/split/test_filter_header_rg.c
+-rw-r--r-- root/root 6815 2015-02-03 00:18 ./usr/share/samtools/test/split/test_parse_args.c
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/stat/
+-rw-r--r-- root/root 61486 2015-02-03 00:18 ./usr/share/samtools/test/stat/1.stats.expected
+-rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/1_map_cigar.sam
+-rw-r--r-- root/root 61485 2015-02-03 00:18 ./usr/share/samtools/test/stat/2.stats.expected
+-rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam
+-rw-r--r-- root/root 60454 2015-02-03 00:18 ./usr/share/samtools/test/stat/3.stats.expected
+-rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam
+-rw-r--r-- root/root 61486 2015-02-03 00:18 ./usr/share/samtools/test/stat/4.stats.expected
+-rw-r--r-- root/root 234 2015-02-03 00:18 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam
+-rw-r--r-- root/root 61508 2015-02-03 00:18 ./usr/share/samtools/test/stat/5.stats.expected
+-rw-r--r-- root/root 236 2015-02-03 00:18 ./usr/share/samtools/test/stat/5_insert_cigar.sam
+-rw-r--r-- root/root 61508 2015-02-03 00:18 ./usr/share/samtools/test/stat/6.stats.expected
+-rw-r--r-- root/root 109 2015-02-03 00:18 ./usr/share/samtools/test/stat/test.fa
+-rw-r--r-- root/root 18 2015-02-03 00:18 ./usr/share/samtools/test/stat/test.fa.fai
+-rw-r--r-- root/root 1990 2015-02-03 00:18 ./usr/share/samtools/test/test.c
+-rw-r--r-- root/root 1361 2015-02-03 00:18 ./usr/share/samtools/test/test.h
+-rwxr-xr-x root/root 83362 2015-02-03 00:18 ./usr/share/samtools/test/test.pl
+drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/tview/
+-rw-r--r-- root/root 2424 2015-02-03 00:18 ./usr/share/samtools/test/tview/test_get_rg_sample.c
+-rw-r--r-- root/root 3455 2015-02-03 00:18 ./usr/share/samtools/test/vcf-miniview.c
+
+
+samtools_1.2-1_amd64.deb
────────────────────────
new debian package, version 2.0.
- size 378168 bytes: control archive=1555 bytes.
+ size 392492 bytes: control archive=1488 bytes.
801 bytes, 16 lines control
1557 bytes, 27 lines md5sums
Package: samtools
- Version: 1.1-1
+ Version: 1.2-1
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1040
+ Installed-Size: 1066
Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1759,298 +2177,41 @@ samtools_1.1-1_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 2014-09-25 09:08 ./
-drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/
-drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/bin/
--rwxr-xr-x root/root 22664 2014-09-25 09:08 ./usr/bin/ace2sam
--rwxr-xr-x root/root 5328 2014-09-20 00:51 ./usr/bin/blast2sam.pl
--rwxr-xr-x root/root 3364 2014-09-20 00:51 ./usr/bin/bowtie2sam.pl
--rwxr-xr-x root/root 18032 2014-09-20 00:51 ./usr/bin/export2sam.pl
--rwxr-xr-x root/root 6125 2014-09-20 00:51 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 10336 2014-09-25 09:08 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10336 2014-09-25 09:08 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14440 2014-09-25 09:08 ./usr/bin/md5fa
--rwxr-xr-x root/root 10280 2014-09-25 09:08 ./usr/bin/md5sum-lite
--rwxr-xr-x root/root 6773 2014-09-20 00:51 ./usr/bin/novo2sam.pl
--rwxr-xr-x root/root 48023 2014-09-20 00:51 ./usr/bin/plot-bamstats
--rwxr-xr-x root/root 3208 2014-09-20 00:51 ./usr/bin/psl2sam.pl
--rwxr-xr-x root/root 8961 2014-09-20 00:51 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 767928 2014-09-25 09:08 ./usr/bin/samtools
--rwxr-xr-x root/root 16478 2014-09-20 00:51 ./usr/bin/samtools.pl
--rwxr-xr-x root/root 10789 2014-09-20 00:51 ./usr/bin/seq_cache_populate.pl
--rwxr-xr-x root/root 3909 2014-09-20 00:51 ./usr/bin/soap2sam.pl
--rwxr-xr-x root/root 7888 2014-09-20 00:51 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 22752 2014-09-25 09:08 ./usr/bin/wgsim
--rwxr-xr-x root/root 4157 2014-09-20 00:51 ./usr/bin/wgsim_eval.pl
--rwxr-xr-x root/root 3583 2014-09-20 00:51 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/share/
-drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/share/doc/
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--rw-r--r-- root/root 828 2014-09-20 00:51 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2014-09-25 08:56 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3270 2014-09-25 09:05 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2014-09-25 08:56 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2014-09-25 08:56 ./usr/share/doc/samtools/reference
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--rw-r--r-- root/root 12774 2014-09-25 09:08 ./usr/share/man/man1/samtools.1.gz
-
-
-samtools-test_1.1-1_all.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 2644466 bytes: control archive=6161 bytes.
- 467 bytes, 14 lines control
- 17627 bytes, 215 lines md5sums
- Package: samtools-test
- Source: samtools
- Version: 1.1-1
- Architecture: all
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9148
- Section: science
- Priority: optional
- Homepage: http://www.htslib.org/
- Description: test files for the samtools package.
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format.
- .
- This package contains test files for the samtools package.
-
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--rw-r--r-- root/root 140 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/expected/75.out
--rw-r--r-- root/root 221725 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/expected/76.out
--rw-r--r-- root/root 318473 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/expected/77.out
--rw-r--r-- root/root 204 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/expected/8.out
--rw-r--r-- root/root 137 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/expected/9.out
--rw-r--r-- root/root 1561 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/indels.sam
-drwxr-xr-x root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/
--rw-r--r-- root/root 200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
--rw-r--r-- root/root 200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
--rw-r--r-- root/root 4200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
--rw-r--r-- root/root 200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
--rw-r--r-- root/root 200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
--rw-r--r-- root/root 200 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
--rw-r--r-- root/root 280 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup-E.bam
--rw-r--r-- root/root 71637 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.1.bam
--rw-r--r-- root/root 776 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.1.bam.bai
--rw-r--r-- root/root 31556 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.2.bam
--rw-r--r-- root/root 31216 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.3.bam
--rw-r--r-- root/root 4284 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.ref.fa
--rw-r--r-- root/root 17 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.ref.fa.fai
--rw-r--r-- root/root 7616 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/mpileup.reg
--rw-r--r-- root/root 793 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/overlap50.sam
--rw-r--r-- root/root 583 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/overlapIllumina.bam
--rw-r--r-- root/root 250 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/regions
--rwxr-xr-x root/root 4376 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/regression.sh
--rw-r--r-- root/root 215 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/xx#minimal.bam
--rw-r--r-- root/root 247 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/xx#triplet.bam
--rw-r--r-- root/root 56 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/xx.fa
--rw-r--r-- root/root 29 2014-09-20 00:51 ./usr/share/samtools/test/mpileup/xx.fa.fai
-drwxr-xr-x root/root 0 2014-09-25 09:08 ./usr/share/samtools/test/split/
--rw-r--r-- root/root 3597 2014-09-20 00:51 ./usr/share/samtools/test/split/test_count_rg.c
--rw-r--r-- root/root 3951 2014-09-20 00:51 ./usr/share/samtools/test/split/test_expand_format_string.c
--rw-r--r-- root/root 5173 2014-09-20 00:51 ./usr/share/samtools/test/split/test_filter_header_rg.c
--rw-r--r-- root/root 6815 2014-09-20 00:51 ./usr/share/samtools/test/split/test_parse_args.c
-drwxr-xr-x root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/stat/
--rw-r--r-- root/root 61473 2014-09-20 00:51 ./usr/share/samtools/test/stat/1.stats.expected
--rw-r--r-- root/root 232 2014-09-20 00:51 ./usr/share/samtools/test/stat/1_map_cigar.sam
--rw-r--r-- root/root 61472 2014-09-20 00:51 ./usr/share/samtools/test/stat/2.stats.expected
--rw-r--r-- root/root 232 2014-09-20 00:51 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam
--rw-r--r-- root/root 60441 2014-09-20 00:51 ./usr/share/samtools/test/stat/3.stats.expected
--rw-r--r-- root/root 232 2014-09-20 00:51 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam
--rw-r--r-- root/root 61473 2014-09-20 00:51 ./usr/share/samtools/test/stat/4.stats.expected
--rw-r--r-- root/root 234 2014-09-20 00:51 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam
--rw-r--r-- root/root 61495 2014-09-20 00:51 ./usr/share/samtools/test/stat/5.stats.expected
--rw-r--r-- root/root 236 2014-09-20 00:51 ./usr/share/samtools/test/stat/5_insert_cigar.sam
--rw-r--r-- root/root 61495 2014-09-20 00:51 ./usr/share/samtools/test/stat/6.stats.expected
--rw-r--r-- root/root 109 2014-09-20 00:51 ./usr/share/samtools/test/stat/test.fa
--rw-r--r-- root/root 18 2014-09-20 00:51 ./usr/share/samtools/test/stat/test.fa.fai
--rw-r--r-- root/root 1990 2014-09-20 00:51 ./usr/share/samtools/test/test.c
--rw-r--r-- root/root 1361 2014-09-20 00:51 ./usr/share/samtools/test/test.h
--rwxr-xr-x root/root 82575 2014-09-25 09:06 ./usr/share/samtools/test/test.pl
-drwxr-xr-x root/root 0 2014-09-20 00:51 ./usr/share/samtools/test/tview/
--rw-r--r-- root/root 2424 2014-09-20 00:51 ./usr/share/samtools/test/tview/test_get_rg_sample.c
--rw-r--r-- root/root 3455 2014-09-20 00:51 ./usr/share/samtools/test/vcf-miniview.c
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/bin/
+-rwxr-xr-x root/root 22664 2015-06-16 06:17 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-03 00:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-03 00:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-03 00:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-03 00:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10336 2015-06-16 06:17 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10336 2015-06-16 06:17 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14440 2015-06-16 06:17 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10280 2015-06-16 06:17 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-03 00:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-03 00:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-03 00:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-03 00:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 806520 2015-06-16 06:17 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-03 00:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-03 00:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-03 00:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-03 00:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22752 2015-06-16 06:17 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-03 00:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-03 00:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-03 00:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-06-15 21:23 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3392 2015-06-16 06:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-06-15 21:30 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-06-15 21:23 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-06-16 06:17 ./usr/share/man/man1/samtools.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2075,114 +2236,118 @@ The following packages will be REMOVED:
gettext-base* groff-base* hardening-includes* intltool-debian*
libapt-pkg-perl* libarchive-zip-perl* libasprintf0c2*
libclass-accessor-perl* libclone-perl* libcroco3* libdigest-hmac-perl*
- libemail-valid-perl* libffi6* libfile-basedir-perl* libglib2.0-0*
- libhts-dev* libhts1* libio-pty-perl* libio-socket-inet6-perl*
- libio-socket-ssl-perl* libio-string-perl* libipc-run-perl*
- liblist-moreutils-perl* libmagic1* libmailtools-perl* libncurses5-dev*
- libnet-dns-perl* libnet-domain-tld-perl* libnet-ip-perl*
- libnet-smtp-ssl-perl* libnet-ssleay-perl* libparse-debianchangelog-perl*
- libpipeline1* libsocket6-perl* libssl1.0.0* libsub-name-perl*
- libtext-levenshtein-perl* libtinfo-dev* libunistring0* liburi-perl* libxml2*
- lintian* man-db* netbase* patchutils* po-debconf*
- sbuild-build-depends-core-dummy* sbuild-build-depends-lintian-dummy*
- sbuild-build-depends-samtools-dummy* t1utils* tabix* zlib1g-dev*
-0 upgraded, 0 newly installed, 58 to remove and 0 not upgraded.
-After this operation, 43.6 MB disk space will be freed.
-(Reading database ... 14528 files and directories currently installed.)
-Removing sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Removing bash-completion (1:2.1-4) ...
-Purging configuration files for bash-completion (1:2.1-4) ...
-Removing sbuild-build-depends-lintian-dummy (0.invalid.0) ...
-Removing lintian (2.5.27) ...
-Purging configuration files for lintian (2.5.27) ...
-Removing debhelper (9.20140817) ...
-Removing man-db (2.7.0.1-1) ...
-Purging configuration files for man-db (2.7.0.1-1) ...
-Removing bsdmainutils (9.0.5) ...
-Purging configuration files for bsdmainutils (9.0.5) ...
-Removing diffstat (1.58-1) ...
-Removing file (1:5.19-2) ...
-Removing po-debconf (1.0.16+nmu3) ...
-Removing intltool-debian (0.35.0+20060710.1) ...
-Removing gettext (0.19.2-2) ...
-Removing gettext-base (0.19.2-2) ...
-Removing groff-base (1.22.2-8) ...
-Purging configuration files for groff-base (1.22.2-8) ...
-Removing hardening-includes (2.5+nmu1) ...
-Removing libapt-pkg-perl (0.1.29+b2) ...
-Removing libarchive-zip-perl (1.38-1) ...
-Removing libasprintf0c2:amd64 (0.19.2-2) ...
-Removing libparse-debianchangelog-perl (1.2.0-1.1) ...
-Removing libclass-accessor-perl (0.34-1) ...
-Removing libclone-perl (0.37-1+b1) ...
-Removing libcroco3:amd64 (0.6.8-3) ...
-Purging configuration files for libcroco3:amd64 (0.6.8-3) ...
-Removing libemail-valid-perl (1.195-1) ...
-Removing libnet-dns-perl (0.79-2) ...
-Removing libdigest-hmac-perl (1.03+dfsg-1) ...
-Removing libglib2.0-0:amd64 (2.42.0-1) ...
-Purging configuration files for libglib2.0-0:amd64 (2.42.0-1) ...
-Removing libffi6:amd64 (3.1-2) ...
-Purging configuration files for libffi6:amd64 (3.1-2) ...
-Removing libfile-basedir-perl (0.03-1) ...
-Removing libhts-dev:amd64 (1.1-1) ...
-Removing libhts1:amd64 (1.1-1) ...
-Purging configuration files for libhts1:amd64 (1.1-1) ...
-Removing libipc-run-perl (0.92-1) ...
-Removing libio-pty-perl (1:1.08-1+b4) ...
-Removing libio-socket-inet6-perl (2.72-1) ...
-Removing libmailtools-perl (2.13-1) ...
-Removing libnet-smtp-ssl-perl (1.01-3) ...
-Removing libio-socket-ssl-perl (1.998-1) ...
-Removing libio-string-perl (1.08-3) ...
-Removing liblist-moreutils-perl (0.33-2+b1) ...
-Removing libmagic1:amd64 (1:5.19-2) ...
-Purging configuration files for libmagic1:amd64 (1:5.19-2) ...
-Removing libncurses5-dev:amd64 (5.9+20140913-1) ...
-Removing libnet-domain-tld-perl (1.72-1) ...
-Removing libnet-ip-perl (1.26-1) ...
-Removing libnet-ssleay-perl (1.65-1+b1) ...
-Removing libpipeline1:amd64 (1.3.1-1) ...
-Purging configuration files for libpipeline1:amd64 (1.3.1-1) ...
-Removing libsocket6-perl (0.25-1+b1) ...
-Removing libssl1.0.0:amd64 (1.0.1i-2) ...
-Purging configuration files for libssl1.0.0:amd64 (1.0.1i-2) ...
-Removing libsub-name-perl (0.07-1+b1) ...
-Removing libtext-levenshtein-perl (0.09-1) ...
-Removing libtinfo-dev:amd64 (5.9+20140913-1) ...
-Removing libunistring0:amd64 (0.9.3-5.2) ...
-Purging configuration files for libunistring0:amd64 (0.9.3-5.2) ...
-Removing liburi-perl (1.64-1) ...
-Removing libxml2:amd64 (2.9.1+dfsg1-4) ...
-Purging configuration files for libxml2:amd64 (2.9.1+dfsg1-4) ...
-Removing netbase (5.2) ...
-Purging configuration files for netbase (5.2) ...
-Removing patchutils (0.3.3-1) ...
-Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
-Removing t1utils (1.37-2.1) ...
-Removing tabix (1.1-1) ...
-Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-2) ...
-Processing triggers for libc-bin (2.19-11) ...
+ libemail-valid-perl* libexporter-tiny-perl* libffi6* libfile-basedir-perl*
+ libglib2.0-0* libhts-dev* libhts1* libicu52* libio-pty-perl*
+ libio-socket-inet6-perl* libio-socket-ssl-perl* libio-string-perl*
+ libipc-run-perl* libipc-system-simple-perl* liblist-moreutils-perl*
+ libmagic1* libmailtools-perl* libncurses5-dev* libnet-dns-perl*
+ libnet-domain-tld-perl* libnet-ip-perl* libnet-smtp-ssl-perl*
+ libnet-ssleay-perl* libparse-debianchangelog-perl* libpipeline1*
+ libsocket6-perl* libssl1.0.0* libsub-name-perl* libtext-levenshtein-perl*
+ libtinfo-dev* libunistring0* libxml2* lintian* man-db* netbase* patchutils*
+ po-debconf* sbuild-build-depends-core-dummy*
+ sbuild-build-depends-lintian-dummy* sbuild-build-depends-samtools-dummy*
+ t1utils* tabix* zlib1g-dev*
+0 upgraded, 0 newly installed, 60 to remove and 0 not upgraded.
+After this operation, 73.8 MB disk space will be freed.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14907 files and directories currently installed.)
+Removing sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Removing bash-completion (1:2.1-4.1) ...
+Purging configuration files for bash-completion (1:2.1-4.1) ...
+Removing sbuild-build-depends-lintian-dummy (0.invalid.0) ...
+Removing lintian (2.5.31) ...
+Purging configuration files for lintian (2.5.31) ...
+Removing debhelper (9.20150507) ...
+Removing man-db (2.7.0.2-5) ...
+Purging configuration files for man-db (2.7.0.2-5) ...
+Removing bsdmainutils (9.0.6) ...
+Purging configuration files for bsdmainutils (9.0.6) ...
+Removing diffstat (1.58-1) ...
+Removing file (1:5.22+15-2) ...
+Removing po-debconf (1.0.18) ...
+Removing intltool-debian (0.35.0+20060710.2) ...
+Removing gettext (0.19.4-1) ...
+Removing gettext-base (0.19.4-1) ...
+Removing groff-base (1.22.3-1) ...
+Purging configuration files for groff-base (1.22.3-1) ...
+Removing hardening-includes (2.7) ...
+Removing libapt-pkg-perl (0.1.29+b2) ...
+Removing libarchive-zip-perl (1.39-1) ...
+Removing libasprintf0c2:amd64 (0.19.4-1) ...
+Removing libparse-debianchangelog-perl (1.2.0-4) ...
+Removing libclass-accessor-perl (0.34-1) ...
+Removing libclone-perl (0.38-1) ...
+Removing libcroco3:amd64 (0.6.8-3+b1) ...
+Purging configuration files for libcroco3:amd64 (0.6.8-3+b1) ...
+Removing libemail-valid-perl (1.195-1) ...
+Removing libnet-dns-perl (0.81-2) ...
+Removing libdigest-hmac-perl (1.03+dfsg-1) ...
+Removing liblist-moreutils-perl (0.410-1) ...
+Removing libexporter-tiny-perl (0.042-1) ...
+Removing libglib2.0-0:amd64 (2.44.1-1) ...
+Purging configuration files for libglib2.0-0:amd64 (2.44.1-1) ...
+Removing libffi6:amd64 (3.1-2+b2) ...
+Purging configuration files for libffi6:amd64 (3.1-2+b2) ...
+Removing libfile-basedir-perl (0.07-1) ...
+Removing libhts-dev:amd64 (1.2.1-1) ...
+Removing libhts1:amd64 (1.2.1-1) ...
+Purging configuration files for libhts1:amd64 (1.2.1-1) ...
+Removing libxml2:amd64 (2.9.2+dfsg1-3) ...
+Purging configuration files for libxml2:amd64 (2.9.2+dfsg1-3) ...
+Removing libicu52:amd64 (52.1-9) ...
+Purging configuration files for libicu52:amd64 (52.1-9) ...
+Removing libipc-run-perl (0.94-1) ...
+Removing libio-pty-perl (1:1.08-1+b4) ...
+Removing libio-socket-inet6-perl (2.72-2) ...
+Removing libmailtools-perl (2.13-1) ...
+Removing libnet-smtp-ssl-perl (1.01-3) ...
+Removing libio-socket-ssl-perl (2.016-1) ...
+Removing libio-string-perl (1.08-3) ...
+Removing libipc-system-simple-perl (1.25-2) ...
+Removing libmagic1:amd64 (1:5.22+15-2) ...
+Purging configuration files for libmagic1:amd64 (1:5.22+15-2) ...
+Removing libncurses5-dev:amd64 (5.9+20150516-2) ...
+Removing libnet-domain-tld-perl (1.73-1) ...
+Removing libnet-ip-perl (1.26-1) ...
+Removing libnet-ssleay-perl (1.68-1) ...
+Removing libpipeline1:amd64 (1.4.0-1) ...
+Purging configuration files for libpipeline1:amd64 (1.4.0-1) ...
+Removing libsocket6-perl (0.25-1+b1) ...
+Removing libssl1.0.0:amd64 (1.0.2c-1) ...
+Purging configuration files for libssl1.0.0:amd64 (1.0.2c-1) ...
+Removing libsub-name-perl (0.12-1) ...
+Removing libtext-levenshtein-perl (0.12-1) ...
+Removing libtinfo-dev:amd64 (5.9+20150516-2) ...
+Removing libunistring0:amd64 (0.9.3-5.2+b1) ...
+Purging configuration files for libunistring0:amd64 (0.9.3-5.2+b1) ...
+Removing netbase (5.3) ...
+Purging configuration files for netbase (5.3) ...
+Removing patchutils (0.3.4-1) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing t1utils (1.38-4) ...
+Removing tabix (1.2.1-1) ...
+Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Processing triggers for libc-bin (2.19-18) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: amd64
-Build-Space: 32068
-Build-Time: 128
+Build-Space: 32080
+Build-Time: 125
Distribution: unstable
Host Architecture: amd64
-Install-Time: 15
-Job: samtools_1.1-1.dsc
+Install-Time: 18
+Job: samtools_1.2-1.dsc
Lintian: pass
Machine Architecture: amd64
Package: samtools
Package-Time: 151
-Source-Version: 1.1-1
-Space: 32068
+Source-Version: 1.2-1
+Space: 32080
Status: successful
-Version: 1.1-1
+Version: 1.2-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0908
-Build needed 00:02:31, 32068k disc space
+Finished at 20150616-0617
+Build needed 00:02:31, 32080k disc space
diff --git a/dsc b/dsc
index a993eb4..c68089b 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, samtools-test
Architecture: any all
-Version: 1.1-1
+Version: 1.2-1
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>, Dominique Belhachemi <domibel at debian.org>
Homepage: http://www.htslib.org/
@@ -13,34 +13,34 @@ Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/samtools.git
Vcs-Git: git://anonscm.debian.org/debian-med/samtools.git
Testsuite: autopkgtest
-Build-Depends: debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
+Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
Package-List:
samtools deb science optional arch=any
samtools-test deb science optional arch=all
Checksums-Sha1:
- ca446ec24eabd2f71605dde55a787f182cb50f13 4320951 samtools_1.1.orig.tar.gz
- 0e4de8be00fb4dd375048b1b1dc05e2f120e2ead 10164 samtools_1.1-1.debian.tar.xz
+ 9fabb4903b9d1521aeea8a5538e64aefe8e85526 4318615 samtools_1.2.orig.tar.gz
+ a91e9483810ed9ed0e979138febf467b6db6956d 9596 samtools_1.2-1.debian.tar.xz
Checksums-Sha256:
- cee231e33b7290be8e07dea43a99b885d9df79d957625ac84879b47ff91cda69 4320951 samtools_1.1.orig.tar.gz
- 50e5d2299c2d99ce53647fc0cb08eee53bc31d08bfa7d7cc981e6fae28ab231b 10164 samtools_1.1-1.debian.tar.xz
+ e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47 4318615 samtools_1.2.orig.tar.gz
+ c3a6bead979cd8bb0b8fec3e9d6b2bb352db21ae4fdac8ad214757aed72bad23 9596 samtools_1.2-1.debian.tar.xz
Files:
- 5fda5c175d04bff39c56078aea7cd3b1 4320951 samtools_1.1.orig.tar.gz
- 40b3a1f31e22323c8d247e1bff1a9c52 10164 samtools_1.1-1.debian.tar.xz
+ 2748356ef392c0694ca1142de37cf2aa 4318615 samtools_1.2.orig.tar.gz
+ af3dbbae0acff0b7f989b54455839b56 9596 samtools_1.2-1.debian.tar.xz
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diff --git a/upload b/upload
index 9ff390e..8e30fa0 100644
--- a/upload
+++ b/upload
@@ -1,7 +1,7 @@
-u samtools_1.1-1_amd64.deb ftp.upload.debian.org Thu Sep 25 09:09:48 2014
-u samtools_1.1-1.debian.tar.xz ftp.upload.debian.org Thu Sep 25 09:09:49 2014
-u samtools-test_1.1-1_all.deb ftp.upload.debian.org Thu Sep 25 09:09:52 2014
-u samtools_1.1-1.dsc ftp.upload.debian.org Thu Sep 25 09:09:54 2014
-u samtools_1.1.orig.tar.gz ftp.upload.debian.org Thu Sep 25 09:09:57 2014
-u samtools_1.1-1_amd64.changes ftp.upload.debian.org Thu Sep 25 09:09:58 2014
-s samtools_1.1-1_amd64.changes ftp.upload.debian.org Thu Sep 25 09:09:58 2014
+u samtools_1.2-1.dsc ftp.upload.debian.org Tue Jun 16 06:53:44 2015
+u samtools_1.2.orig.tar.gz ftp.upload.debian.org Tue Jun 16 06:53:48 2015
+u samtools_1.2-1_amd64.deb ftp.upload.debian.org Tue Jun 16 06:53:50 2015
+u samtools_1.2-1.debian.tar.xz ftp.upload.debian.org Tue Jun 16 06:53:51 2015
+u samtools-test_1.2-1_all.deb ftp.upload.debian.org Tue Jun 16 06:53:55 2015
+u samtools_1.2-1_amd64.changes ftp.upload.debian.org Tue Jun 16 06:53:56 2015
+s samtools_1.2-1_amd64.changes ftp.upload.debian.org Tue Jun 16 06:53:56 2015
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git
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