[med-svn] samtools 01/01: samtools (1.2-2) unstable; urgency=medium
Charles Plessy
plessy at moszumanska.debian.org
Thu Sep 17 11:38:24 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 18245138e3cc7f0d9f6fbe9cdc2381374e21074a
Author: Charles Plessy <plessy at debian.org>
Date: Thu Sep 17 20:38:08 2015 +0900
samtools (1.2-2) unstable; urgency=medium
[ Afif Elghraoui ]
eb56918 Add patch to fix building on i386
702d289 Remove source files not present in upstream tarball
7afd302 Allow all scripts to be called without language extensions
[ Charles Plessy ]
876f680 Document the update workflow of the source package's repository.
-- Charles Plessy <plessy at debian.org> Thu, 17 Sep 2015 20:21:15 +0900
---
amd64.changes | 72 +++--
amd64.log | 970 ++++++++++++++++++++++------------------------------------
dsc | 34 +-
upload | 13 +-
4 files changed, 422 insertions(+), 667 deletions(-)
diff --git a/amd64.changes b/amd64.changes
index e9876d9..da52cb8 100644
--- a/amd64.changes
+++ b/amd64.changes
@@ -2,11 +2,11 @@
Hash: SHA512
Format: 1.8
-Date: Tue, 16 Jun 2015 06:12:12 +0900
+Date: Thu, 17 Sep 2015 20:21:15 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: source all amd64
-Version: 1.2-1
+Version: 1.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -15,47 +15,45 @@ Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package.
Changes:
- samtools (1.2-1) unstable; urgency=medium
+ samtools (1.2-2) 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.
+ [ Afif Elghraoui ]
+ eb56918 Add patch to fix building on i386
+ 702d289 Remove source files not present in upstream tarball
+ 7afd302 Allow all scripts to be called without language extensions
+ .
+ [ Charles Plessy ]
+ 876f680 Document the update workflow of the source package's repository.
Checksums-Sha1:
- 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
+ 466308992c8332e39e607b2ea582bd233e0ca2d8 2117 samtools_1.2-2.dsc
+ 67060d378093df98a1a5e579f8aa717f7d820ddb 9660 samtools_1.2-2.debian.tar.xz
+ 42c12bab33f018b73d97617f54c6820a1fb32fa8 2646396 samtools-test_1.2-2_all.deb
+ ceed8d67a37aef4352f4134fdabc585cbfa04a41 75450 samtools_1.2-2_amd64.deb
Checksums-Sha256:
- 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
+ 6b054a0967882dc98e2f81b0257ce26980d30d3a60ed878a0bec1ea0d90a188c 2117 samtools_1.2-2.dsc
+ 45e989172a110c980a50380e13979eec78d982b75ddccae33f1c6f4e931ef686 9660 samtools_1.2-2.debian.tar.xz
+ 8fc146560ecf3658e7287128ffc4f54c224f810c03e0a7565f0c3b595997ba12 2646396 samtools-test_1.2-2_all.deb
+ 5228feb9b9d48c2ce843420266760c224e1e14758671b6c82e0c4009bc73a35f 75450 samtools_1.2-2_amd64.deb
Files:
- 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
+ 1cc68f090a1ad2b0e0624e187c380073 2117 science optional samtools_1.2-2.dsc
+ 042d3648bfecb640ddca7a9ab34033c4 9660 science optional samtools_1.2-2.debian.tar.xz
+ 19dc121013e77df2f8d64d5bb954031a 2646396 science optional samtools-test_1.2-2_all.deb
+ 4c2ad525426b028fb47ea329de21da6c 75450 science optional samtools_1.2-2_amd64.deb
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diff --git a/amd64.log b/amd64.log
index d8368c5..9db22ca 100644
--- a/amd64.log
+++ b/amd64.log
@@ -1,30 +1,30 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on aqwa.igloo
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bubu.igloo
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-1 (amd64) 16 juin 2015 06:14 ║
+║ samtools 1.2-2 (amd64) 17 sept. 2015 20:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-1
-Source Version: 1.2-1
+Version: 1.2-2
+Source Version: 1.2-2
Distribution: unstable
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-Ii1pvw/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-Ii1pvw' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-de96647b-ea47-4cc5-9307-b2629755ee00' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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 (12.7 kB/s)
+Hit http://ftp2.jp.debian.org sid InRelease
+Get:1 http://ftp2.jp.debian.org sid/main Sources/DiffIndex [7876 B]
+Get:2 http://ftp2.jp.debian.org sid/main amd64 Packages/DiffIndex [7876 B]
+Get:3 http://ftp2.jp.debian.org sid/main Translation-en/DiffIndex [7876 B]
+Fetched 23.6 kB in 1s (14.6 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
@@ -39,7 +39,7 @@ Reading state information...
Local sources
─────────────
-samtools_1.2-1.dsc exists in .; copying to chroot
+samtools_1.2-2.dsc exists in .; copying to chroot
Check architectures
───────────────────
@@ -50,7 +50,7 @@ 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-GsDMvZ/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-82t7xC/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
@@ -71,16 +71,16 @@ 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/772 B of archives.
+Need to get 0 B/776 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 ...
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(Reading database ... 11516 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 11894 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'.
+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 (>= 4:5.2), g++ (>= 4:5.2), 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 (>= 4:5.2), g++ (>= 4:5.2), 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-rMzyPf/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Ign file: ./ InRelease
Get:1 file: ./ Release.gpg [299 B]
@@ -99,89 +99,96 @@ Building dependency tree...
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 libicu52 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ 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
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
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 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]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ 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, 26 newly installed, 0 to remove and 0 not upgraded.
+Need to get 12.5 MB/18.3 MB of archives.
+After this operation, 65.3 MB of additional disk space will be used.
+Get:1 http://ftp2.jp.debian.org/debian/ sid/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://ftp2.jp.debian.org/debian/ sid/main man-db amd64 2.7.3-1 [1001 kB]
+Get:3 http://ftp2.jp.debian.org/debian/ sid/main libicu55 amd64 55.1-5 [7651 kB]
+Get:4 http://ftp2.jp.debian.org/debian/ sid/main libxml2 amd64 2.9.2+really2.9.1+dfsg1-0.2 [905 kB]
+Get:5 http://ftp2.jp.debian.org/debian/ sid/main libmagic1 amd64 1:5.24-2 [255 kB]
+Get:6 http://ftp2.jp.debian.org/debian/ sid/main file amd64 1:5.24-2 [61.2 kB]
+Get:7 http://ftp2.jp.debian.org/debian/ sid/main gettext-base amd64 0.19.6-1 [123 kB]
+Get:8 http://ftp2.jp.debian.org/debian/ sid/main gettext amd64 0.19.6-1 [1468 kB]
+Get:9 http://ftp2.jp.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:10 http://ftp2.jp.debian.org/debian/ sid/main libhts-dev amd64 1.2.1-1 [278 kB]
+Get:11 http://ftp2.jp.debian.org/debian/ sid/main libio-pty-perl amd64 1:1.08-1+b4 [35.8 kB]
+Get:12 http://ftp2.jp.debian.org/debian/ sid/main libtinfo-dev amd64 6.0+20150810-1 [77.5 kB]
+Get:13 http://ftp2.jp.debian.org/debian/ sid/main libncurses5-dev amd64 6.0+20150810-1 [172 kB]
+Get:14 http://ftp2.jp.debian.org/debian/ sid/main tabix amd64 1.2.1-1 [223 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 910 kB in 0s (1474 kB/s)
-Selecting previously unselected package libpipeline1:amd64.
-(Reading database ...
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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) ...
+Fetched 12.5 MB in 12s (971 kB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11894 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
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 libpipeline1:amd64.
+Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.1-1) ...
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) ...
+Preparing to unpack .../man-db_2.7.3-1_amd64.deb ...
+Unpacking man-db (2.7.3-1) ...
Selecting previously unselected package libffi6:amd64.
-Preparing to unpack .../libffi6_3.1-2+b2_amd64.deb ...
-Unpacking libffi6:amd64 (3.1-2+b2) ...
+Preparing to unpack .../libffi6_3.2.1-3_amd64.deb ...
+Unpacking libffi6:amd64 (3.2.1-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:amd64.
+Preparing to unpack .../libicu55_55.1-5_amd64.deb ...
+Unpacking libicu55:amd64 (55.1-5) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.2+really2.9.1+dfsg1-0.2_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
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 libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.24-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.24-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.22+15-2_amd64.deb ...
-Unpacking file (1:5.22+15-2) ...
+Preparing to unpack .../file_1%3a5.24-2_amd64.deb ...
+Unpacking file (1:5.24-2) ...
Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.4-1_amd64.deb ...
-Unpacking gettext-base (0.19.4-1) ...
+Preparing to unpack .../gettext-base_0.19.6-1_amd64.deb ...
+Unpacking gettext-base (0.19.6-1) ...
Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.4-1_amd64.deb ...
-Unpacking gettext (0.19.4-1) ...
+Preparing to unpack .../gettext_0.19.6-1_amd64.deb ...
+Unpacking gettext (0.19.6-1) ...
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) ...
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
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) ...
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
Selecting previously unselected package libhts1:amd64.
Preparing to unpack .../libhts1_1.2.1-1_amd64.deb ...
Unpacking libhts1:amd64 (1.2.1-1) ...
@@ -192,11 +199,11 @@ 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) ...
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_amd64.deb ...
+Unpacking libtinfo-dev:amd64 (6.0+20150810-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (6.0+20150810-1) ...
Selecting previously unselected package tabix.
Preparing to unpack .../tabix_1.2.1-1_amd64.deb ...
Unpacking tabix (1.2.1-1) ...
@@ -206,46 +213,45 @@ 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 bash-completion (1:2.1-4.2) ...
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) ...
+Setting up libpipeline1:amd64 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
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) ...
+Setting up libffi6:amd64 (3.2.1-3) ...
+Setting up libglib2.0-0:amd64 (2.44.1-1.1) ...
No schema files found: doing nothing.
+Setting up libicu55:amd64 (55.1-5) ...
+Setting up libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
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 libmagic1:amd64 (1:5.24-2) ...
+Setting up file (1:5.24-2) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.18) ...
-Setting up debhelper (9.20150507) ...
+Setting up debhelper (9.20150811) ...
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 libtinfo-dev:amd64 (6.0+20150810-1) ...
+Setting up libncurses5-dev:amd64 (6.0+20150810-1) ...
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) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [...]
+Kernel: Linux 4.1.0-0.bpo.2-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -255,13 +261,13 @@ Package versions: apt_1.0.9.10 base-files_9.2 base-passwd_3.5.37 bash_4.3-12 bas
Unpack source
─────────────
-dpkg-source: warning: extracting unsigned source package (samtools_1.2-1.dsc)
+dpkg-source: warning: extracting unsigned source package (samtools_1.2-2.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: unpacking samtools_1.2-2.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
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -272,14 +278,17 @@ User Environment
────────────────
HOME=/sbuild-nonexistent
+LD_LIBRARY_PATH=/usr/lib/libeatmydata
+LD_PRELOAD=libeatmydata.so
LOGNAME=charles
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
-SCHROOT_CHROOT_NAME=unstable-amd64-sbuild
+PWD=/«PKGBUILDDIR»
+SCHROOT_ALIAS_NAME=unstable
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=unstable-amd64-sbuild-f5de7d7c-936b-47a6-bda9-e4ff8c4e4fc1
+SCHROOT_SESSION_ID=sid-amd64-sbuild-de96647b-ea47-4cc5-9307-b2629755ee00
SCHROOT_UID=1000
SCHROOT_USER=charles
SHELL=/bin/sh
@@ -288,14 +297,14 @@ USER=charles
USERNAME=charles
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT=seat0
-XDG_SESSION_ID=3
+XDG_SESSION_ID=1
XDG_VTNR=7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-1
+dpkg-buildpackage: source version 1.2-2
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
dpkg-source --before-build samtools-1.2
@@ -303,8 +312,8 @@ dpkg-buildpackage: host architecture amd64
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
- dh_auto_clean -O--parallel
+ dh_testdir
+ dh_auto_clean
make -j1 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
@@ -313,13 +322,14 @@ rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f TAGS
make[1]: Leaving directory '/«PKGBUILDDIR»'
- dh_clean -O--parallel
+ dh_clean
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
rm -f debian/samtools-test.substvars
rm -f debian/samtools-test.*.debhelper
rm -rf debian/samtools-test/
+ rm -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
@@ -335,16 +345,12 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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-1.2/.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
+dpkg-source: info: building samtools in samtools_1.2-2.debian.tar.xz
+dpkg-source: info: building samtools in samtools_1.2-2.dsc
debian/rules build
dh build --parallel
- dh_testdir -O--parallel
- dh_auto_configure -O--parallel
+ dh_testdir
+ dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
@@ -443,82 +449,82 @@ 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/bIZ9VxwNgp/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/FL8pW6xlSN/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/bIZ9VxwNgp/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/FL8pW6xlSN/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/bIZ9VxwNgp/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/FL8pW6xlSN/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/bIZ9VxwNgp/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/bIZ9VxwNgp/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/FL8pW6xlSN/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/bIZ9VxwNgp/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/FL8pW6xlSN/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/bIZ9VxwNgp/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/FL8pW6xlSN/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/bIZ9VxwNgp/mpileup.bam.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/FL8pW6xlSN/mpileup.bam.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/FL8pW6xlSN/mpileup.bam.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/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/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/mpileup.cram.list -f /tmp/bIZ9VxwNgp/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/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:1050-1060 /tmp/FL8pW6xlSN/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/bIZ9VxwNgp/mpileup.ref.fa.gz -r17:1050-1060 /tmp/bIZ9VxwNgp/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:1050-1060 /tmp/FL8pW6xlSN/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -748,80 +754,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/bIZ9VxwNgp/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/bIZ9VxwNgp/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.test067.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test067.sam -h -l Library 2 /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.test069.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test069.sam -h -l Library 2 /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.test071.sam -h -l Library 2 /tmp/bIZ9VxwNgp/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test071.sam -h -l Library 2 /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/view.test006.cram
.. expected failure
@@ -1322,28 +1328,28 @@ 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/bIZ9VxwNgp/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/FL8pW6xlSN/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/bIZ9VxwNgp/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/FL8pW6xlSN/depad.001p.bam
.. expected failure
@@ -1381,7 +1387,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/wud9kRQhJZ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/zC4zgzSqm5 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1444,8 +1450,8 @@ make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary
dh binary --parallel
- dh_testroot -O--parallel
- dh_prep -O--parallel
+ dh_testroot
+ dh_prep
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -1473,15 +1479,20 @@ cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*a
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/«PKGBUILDDIR»'
+for script in /«PKGBUILDDIR»/debian/tmp/usr/bin/*.*; \
+do \
+ mv $script ${script%.*}; \
+ ln -s `basename ${script%.*}` $script; \
+done
make[1]: Leaving directory '/«PKGBUILDDIR»'
- dh_install -O--parallel
+ dh_install
install -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d 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 --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/
- dh_installdocs -O--parallel
+ dh_installdocs
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
@@ -1492,20 +1503,46 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ dh_installchangelogs
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
+ dh_installman
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
- dh_perl -O--parallel
+ dh_perl
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
(grep -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl) > debian/samtools-test.substvars.new
mv debian/samtools-test.substvars.new debian/samtools-test.substvars
- dh_link -O--parallel
- dh_compress -O--parallel
+ dh_link
+ rm -f debian/samtools/usr/bin/interpolate_sam.pl
+ ln -sf interpolate_sam debian/samtools/usr/bin/interpolate_sam.pl
+ rm -f debian/samtools/usr/bin/bowtie2sam.pl
+ ln -sf bowtie2sam debian/samtools/usr/bin/bowtie2sam.pl
+ rm -f debian/samtools/usr/bin/export2sam.pl
+ ln -sf export2sam debian/samtools/usr/bin/export2sam.pl
+ rm -f debian/samtools/usr/bin/sam2vcf.pl
+ ln -sf sam2vcf debian/samtools/usr/bin/sam2vcf.pl
+ rm -f debian/samtools/usr/bin/soap2sam.pl
+ ln -sf soap2sam debian/samtools/usr/bin/soap2sam.pl
+ rm -f debian/samtools/usr/bin/novo2sam.pl
+ ln -sf novo2sam debian/samtools/usr/bin/novo2sam.pl
+ rm -f debian/samtools/usr/bin/blast2sam.pl
+ ln -sf blast2sam debian/samtools/usr/bin/blast2sam.pl
+ rm -f debian/samtools/usr/bin/psl2sam.pl
+ ln -sf psl2sam debian/samtools/usr/bin/psl2sam.pl
+ rm -f debian/samtools/usr/bin/samtools.pl
+ ln -sf samtools debian/samtools/usr/bin/samtools.pl
+ rm -f debian/samtools/usr/bin/wgsim_eval.pl
+ ln -sf wgsim_eval debian/samtools/usr/bin/wgsim_eval.pl
+ rm -f debian/samtools/usr/bin/zoom2sam.pl
+ ln -sf zoom2sam debian/samtools/usr/bin/zoom2sam.pl
+ rm -f debian/samtools/usr/bin/varfilter.py
+ ln -sf varfilter debian/samtools/usr/bin/varfilter.py
+ rm -f debian/samtools/usr/bin/seq_cache_populate.pl
+ ln -sf seq_cache_populate debian/samtools/usr/bin/seq_cache_populate.pl
+ dh_compress
cd debian/samtools
chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
@@ -1514,7 +1551,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
chmod a-x usr/share/doc/samtools-test/changelog.Debian
gzip -9nf usr/share/doc/samtools-test/changelog.Debian
cd '/«PKGBUILDDIR»'
- dh_fixperms -O--parallel
+ dh_fixperms
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 0644
@@ -1538,24 +1575,23 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ dh_strip
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
- dh_makeshlibs -O--parallel
+ dh_makeshlibs
rm -f debian/samtools/DEBIAN/shlibs
rm -f debian/samtools-test/DEBIAN/shlibs
- dh_shlibdeps -O--parallel
+ dh_shlibdeps
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/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)
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim 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/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam 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
+ dh_installdeb
+ dh_gencontrol
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
@@ -1570,25 +1606,25 @@ dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is no
dpkg-gencontrol: warning: package samtools-test: unused substitution variable ${perl:Depends}
chmod 0644 debian/samtools-test/DEBIAN/control
chown 0:0 debian/samtools-test/DEBIAN/control
- dh_md5sums -O--parallel
+ dh_md5sums
(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 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 0644 debian/samtools-test/DEBIAN/md5sums
chown 0:0 debian/samtools-test/DEBIAN/md5sums
- dh_builddeb -O--parallel
+ dh_builddeb
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-1_amd64.deb'.
+dpkg-deb: building package 'samtools' in '../samtools_1.2-2_amd64.deb'.
dpkg-deb --build debian/samtools-test ..
-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-deb: building package 'samtools-test' in '../samtools-test_1.2-2_all.deb'.
+ dpkg-genchanges >../samtools_1.2-2_amd64.changes
+dpkg-genchanges: not including original source code in upload
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)
+dpkg-buildpackage: binary and diff upload (original source NOT included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150616-0617
+Build finished at 20150917-2025
Finished
────────
@@ -1600,261 +1636,20 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-lintian
-───────
-
-Merged Build-Depends: lintian
-Filtered Build-Depends: lintian
-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...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install lintian build dependencies (apt-based resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Installing build dependencies
-Reading package lists...
-Building dependency tree...
-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
- libexporter-tiny-perl libfile-basedir-perl libio-socket-inet6-perl
- libio-socket-ssl-perl libio-string-perl libipc-run-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 lintian netbase patchutils t1utils
-Suggested packages:
- 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
- libexporter-tiny-perl libfile-basedir-perl libio-socket-inet6-perl
- libio-socket-ssl-perl libio-string-perl libipc-run-perl
- libipc-system-simple-perl liblist-moreutils-perl libmailtools-perl
- libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl
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-I: samtools source: quilt-patch-using-template-description debian-changes
-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
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-W: samtools: script-with-language-extension usr/bin/wgsim_eval.pl
-W: samtools: script-with-language-extension usr/bin/zoom2sam.pl
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:30
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:32
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:46
-I: samtools: spelling-error-in-manpage usr/share/man/man1/samtools.1.gz allows to allows one to
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:144
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:171
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:174
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:433
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:605
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:741
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz:911
-I: samtools: hyphen-used-as-minus-sign usr/share/man/man1/samtools.1.gz 16 more occurrences not shown
-W: samtools: binary-without-manpage usr/bin/ace2sam
-W: samtools: binary-without-manpage usr/bin/blast2sam.pl
-W: samtools: binary-without-manpage usr/bin/bowtie2sam.pl
-W: samtools: binary-without-manpage usr/bin/export2sam.pl
-W: samtools: binary-without-manpage usr/bin/interpolate_sam.pl
-W: samtools: binary-without-manpage usr/bin/maq2sam-long
-W: samtools: binary-without-manpage usr/bin/maq2sam-short
-W: samtools: binary-without-manpage usr/bin/md5fa
-W: samtools: binary-without-manpage usr/bin/md5sum-lite
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-W: samtools: binary-without-manpage usr/bin/sam2vcf.pl
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-W: samtools: binary-without-manpage usr/bin/soap2sam.pl
-W: samtools: binary-without-manpage usr/bin/varfilter.py
-W: samtools: binary-without-manpage usr/bin/wgsim
-W: samtools: binary-without-manpage usr/bin/wgsim_eval.pl
-W: samtools: binary-without-manpage usr/bin/zoom2sam.pl
-
-I: Lintian run was successful.
-
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-1_amd64.changes:
+samtools_1.2-2_amd64.changes:
─────────────────────────────
Format: 1.8
-Date: Tue, 16 Jun 2015 06:12:12 +0900
+Date: Thu, 17 Sep 2015 20:21:15 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: source all amd64
-Version: 1.2-1
+Version: 1.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
@@ -1863,48 +1658,46 @@ Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package.
Changes:
- samtools (1.2-1) unstable; urgency=medium
+ samtools (1.2-2) unstable; urgency=medium
+ .
+ [ Afif Elghraoui ]
+ eb56918 Add patch to fix building on i386
+ 702d289 Remove source files not present in upstream tarball
+ 7afd302 Allow all scripts to be called without language extensions
.
- 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 ]
+ 876f680 Document the update workflow of the source package's repository.
Checksums-Sha1:
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- 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
+ a485f12b5d4ae124d677ef76e21219b3dbc81f1b 1248 samtools_1.2-2.dsc
+ 67060d378093df98a1a5e579f8aa717f7d820ddb 9660 samtools_1.2-2.debian.tar.xz
+ 42c12bab33f018b73d97617f54c6820a1fb32fa8 2646396 samtools-test_1.2-2_all.deb
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- 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
+ 74d34f20c9e8d401ebf2ee028f81114618fcf353406afa40bca593bcbd6166cc 1248 samtools_1.2-2.dsc
+ 45e989172a110c980a50380e13979eec78d982b75ddccae33f1c6f4e931ef686 9660 samtools_1.2-2.debian.tar.xz
+ 8fc146560ecf3658e7287128ffc4f54c224f810c03e0a7565f0c3b595997ba12 2646396 samtools-test_1.2-2_all.deb
+ 5228feb9b9d48c2ce843420266760c224e1e14758671b6c82e0c4009bc73a35f 75450 samtools_1.2-2_amd64.deb
Files:
- 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
+ bc235ec04c9c2d2016d5cfcb49d98ada 1248 science optional samtools_1.2-2.dsc
+ 042d3648bfecb640ddca7a9ab34033c4 9660 science optional samtools_1.2-2.debian.tar.xz
+ 19dc121013e77df2f8d64d5bb954031a 2646396 science optional samtools-test_1.2-2_all.deb
+ 4c2ad525426b028fb47ea329de21da6c 75450 science optional samtools_1.2-2_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-test_1.2-1_all.deb
+samtools-test_1.2-2_all.deb
───────────────────────────
new debian package, version 2.0.
- size 2644688 bytes: control archive=5620 bytes.
+ size 2646396 bytes: control archive=5623 bytes.
494 bytes, 15 lines control
17627 bytes, 215 lines md5sums
Package: samtools-test
Source: samtools
- Version: 1.2-1
+ Version: 1.2-2
Architecture: all
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Installed-Size: 9222
@@ -1918,15 +1711,15 @@ samtools-test_1.2-1_all.deb
.
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 2015-09-17 20:25 ./
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/samtools-test/
+-rw-r--r-- root/root 3542 2015-09-17 20:22 ./usr/share/doc/samtools-test/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-17 20:15 ./usr/share/doc/samtools-test/copyright
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
@@ -1991,7 +1784,7 @@ drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/fixmat
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/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
@@ -2001,7 +1794,7 @@ drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/merge/
-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/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
@@ -2025,7 +1818,7 @@ drwxr-xr-x root/root 0 2015-06-16 06:17 ./usr/share/samtools/test/mpileu
-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/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
@@ -2126,7 +1919,7 @@ drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileu
-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/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
@@ -2153,19 +1946,19 @@ drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/tview/
-rw-r--r-- root/root 3455 2015-02-03 00:18 ./usr/share/samtools/test/vcf-miniview.c
-samtools_1.2-1_amd64.deb
+samtools_1.2-2_amd64.deb
────────────────────────
new debian package, version 2.0.
- size 392492 bytes: control archive=1488 bytes.
- 801 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 75450 bytes: control archive=1426 bytes.
+ 764 bytes, 16 lines control
+ 1467 bytes, 26 lines md5sums
Package: samtools
- Version: 1.2-1
+ Version: 1.2-2
Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1066
- Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 291
+ Depends: libc6 (>= 2.14), libhts1 (>= 1.0), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -2177,41 +1970,53 @@ samtools_1.2-1_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 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
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/bin/
+-rwxr-xr-x root/root 22664 2015-09-17 20:25 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-03 00:18 ./usr/bin/blast2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/blast2sam.pl -> blast2sam
+-rwxr-xr-x root/root 3364 2015-02-03 00:18 ./usr/bin/bowtie2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/bowtie2sam.pl -> bowtie2sam
+-rwxr-xr-x root/root 18032 2015-02-03 00:18 ./usr/bin/export2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/export2sam.pl -> export2sam
+-rwxr-xr-x root/root 6125 2015-02-03 00:18 ./usr/bin/interpolate_sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/interpolate_sam.pl -> interpolate_sam
+-rwxr-xr-x root/root 10336 2015-09-17 20:25 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10336 2015-09-17 20:25 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14440 2015-09-17 20:25 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10280 2015-09-17 20:25 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-03 00:18 ./usr/bin/novo2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/novo2sam.pl -> novo2sam
-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/
+-rwxr-xr-x root/root 3208 2015-02-03 00:18 ./usr/bin/psl2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/psl2sam.pl -> psl2sam
+-rwxr-xr-x root/root 8961 2015-02-03 00:18 ./usr/bin/sam2vcf
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/sam2vcf.pl -> sam2vcf
+-rwxr-xr-x root/root 16478 2015-02-03 00:18 ./usr/bin/samtools
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/samtools.pl -> samtools
+-rwxr-xr-x root/root 11105 2015-02-03 00:18 ./usr/bin/seq_cache_populate
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/seq_cache_populate.pl -> seq_cache_populate
+-rwxr-xr-x root/root 3909 2015-02-03 00:18 ./usr/bin/soap2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/soap2sam.pl -> soap2sam
+-rwxr-xr-x root/root 7888 2015-02-03 00:18 ./usr/bin/varfilter
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/varfilter.py -> varfilter
+-rwxr-xr-x root/root 22752 2015-09-17 20:25 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-03 00:18 ./usr/bin/wgsim_eval
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/wgsim_eval.pl -> wgsim_eval
+-rwxr-xr-x root/root 3583 2015-02-03 00:18 ./usr/bin/zoom2sam
+lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/zoom2sam.pl -> zoom2sam
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./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
+-rw-r--r-- root/root 1031 2015-09-17 20:15 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3542 2015-09-17 20:22 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-17 20:15 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-17 20:15 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-17 20:25 ./usr/share/man/man1/samtools.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2232,122 +2037,75 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
- bash-completion* bsdmainutils* debhelper* diffstat* file* gettext*
- 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* 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.)
+ bash-completion* bsdmainutils* debhelper* file* gettext* gettext-base*
+ groff-base* intltool-debian* libcroco3* libffi6* libglib2.0-0* libhts-dev*
+ libhts1* libicu55* libio-pty-perl* libmagic1* libncurses5-dev* libpipeline1*
+ libtinfo-dev* libunistring0* libxml2* man-db* po-debconf*
+ sbuild-build-depends-core-dummy* sbuild-build-depends-samtools-dummy* tabix*
+ zlib1g-dev*
+0 upgraded, 0 newly installed, 27 to remove and 0 not upgraded.
+After this operation, 65.3 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 ... 14078 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 bash-completion (1:2.1-4.2) ...
+Purging configuration files for bash-completion (1:2.1-4.2) ...
+Removing debhelper (9.20150811) ...
+Removing man-db (2.7.3-1) ...
+Purging configuration files for man-db (2.7.3-1) ...
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 file (1:5.24-2) ...
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 intltool-debian (0.35.0+20060710.4) ...
+Removing gettext (0.19.6-1) ...
+Removing gettext-base (0.19.6-1) ...
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 libglib2.0-0:amd64 (2.44.1-1.1) ...
+Purging configuration files for libglib2.0-0:amd64 (2.44.1-1.1) ...
+Removing libffi6:amd64 (3.2.1-3) ...
+Purging configuration files for libffi6:amd64 (3.2.1-3) ...
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 libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
+Purging configuration files for libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
+Removing libicu55:amd64 (55.1-5) ...
+Purging configuration files for libicu55:amd64 (55.1-5) ...
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 libmagic1:amd64 (1:5.24-2) ...
+Purging configuration files for libmagic1:amd64 (1:5.24-2) ...
+Removing libncurses5-dev:amd64 (6.0+20150810-1) ...
+Removing libpipeline1:amd64 (1.4.1-1) ...
+Purging configuration files for libpipeline1:amd64 (1.4.1-1) ...
+Removing libtinfo-dev:amd64 (6.0+20150810-1) ...
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) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: amd64
-Build-Space: 32080
-Build-Time: 125
+Build-Space: 24836
+Build-Time: 66
Distribution: unstable
Host Architecture: amd64
-Install-Time: 18
-Job: samtools_1.2-1.dsc
-Lintian: pass
+Install-Time: 20
+Job: samtools_1.2-2.dsc
Machine Architecture: amd64
Package: samtools
-Package-Time: 151
-Source-Version: 1.2-1
-Space: 32080
+Package-Time: 89
+Source-Version: 1.2-2
+Space: 24836
Status: successful
-Version: 1.2-1
+Version: 1.2-2
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150616-0617
-Build needed 00:02:31, 32080k disc space
+Finished at 20150917-2025
+Build needed 00:01:29, 24836k disc space
diff --git a/dsc b/dsc
index c68089b..a82b1bb 100644
--- a/dsc
+++ b/dsc
@@ -5,7 +5,7 @@ Format: 3.0 (quilt)
Source: samtools
Binary: samtools, samtools-test
Architecture: any all
-Version: 1.2-1
+Version: 1.2-2
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/
@@ -19,28 +19,28 @@ Package-List:
samtools-test deb science optional arch=all
Checksums-Sha1:
9fabb4903b9d1521aeea8a5538e64aefe8e85526 4318615 samtools_1.2.orig.tar.gz
- a91e9483810ed9ed0e979138febf467b6db6956d 9596 samtools_1.2-1.debian.tar.xz
+ 67060d378093df98a1a5e579f8aa717f7d820ddb 9660 samtools_1.2-2.debian.tar.xz
Checksums-Sha256:
e4be60ad24fe0324b9384fe58ec2ab7359fe926fbee3115d869c447eb01a9e47 4318615 samtools_1.2.orig.tar.gz
- c3a6bead979cd8bb0b8fec3e9d6b2bb352db21ae4fdac8ad214757aed72bad23 9596 samtools_1.2-1.debian.tar.xz
+ 45e989172a110c980a50380e13979eec78d982b75ddccae33f1c6f4e931ef686 9660 samtools_1.2-2.debian.tar.xz
Files:
2748356ef392c0694ca1142de37cf2aa 4318615 samtools_1.2.orig.tar.gz
- af3dbbae0acff0b7f989b54455839b56 9596 samtools_1.2-1.debian.tar.xz
+ 042d3648bfecb640ddca7a9ab34033c4 9660 samtools_1.2-2.debian.tar.xz
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diff --git a/upload b/upload
index 8e30fa0..add57a6 100644
--- a/upload
+++ b/upload
@@ -1,7 +1,6 @@
-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
+u samtools_1.2-2.dsc ftp.upload.debian.org Thu Sep 17 20:29:12 2015
+u samtools_1.2-2_amd64.deb ftp.upload.debian.org Thu Sep 17 20:29:15 2015
+u samtools-test_1.2-2_all.deb ftp.upload.debian.org Thu Sep 17 20:29:25 2015
+u samtools_1.2-2.debian.tar.xz ftp.upload.debian.org Thu Sep 17 20:29:27 2015
+u samtools_1.2-2_amd64.changes ftp.upload.debian.org Thu Sep 17 20:29:28 2015
+s samtools_1.2-2_amd64.changes ftp.upload.debian.org Thu Sep 17 20:29:28 2015
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git
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