[med-svn] samtools 02/04: Build logs for version 1.2-4.
Charles Plessy
plessy at moszumanska.debian.org
Wed Apr 27 00:55:15 UTC 2016
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 8723ad5b92ca8a58f99895976a8bce78f326ddd6
Author: Charles Plessy <plessy at debian.org>
Date: Wed Apr 27 09:51:12 2016 +0900
Build logs for version 1.2-4.
---
arm64.log | 778 +++++++++++++++++++++++++++------------------
armel.log | 782 +++++++++++++++++++++++++++------------------
i386.log | 779 +++++++++++++++++++++++++++------------------
kfreebsd-amd64.log | 769 +++++++++++++++++++++++++++------------------
kfreebsd-i386.log | 761 ++++++++++++++++++++++++++------------------
m68k.log | 106 +++++++
mips64el.log | 907 +++++++++++++++++++++++++++++++++++++----------------
mipsel.log | 788 ++++++++++++++++++++++++++++------------------
ppc64el.log | 777 +++++++++++++++++++++++++++------------------
x32.log => sh4.log | 780 ++++++++++++++++++++++++---------------------
x32.log | 675 +++++++++++++++++++++++++--------------
11 files changed, 4905 insertions(+), 2997 deletions(-)
diff --git a/arm64.log b/arm64.log
index e0e0b3f..a74d73d 100644
--- a/arm64.log
+++ b/arm64.log
@@ -2,45 +2,46 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-arm-03.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (arm64) 22 Sep 2015 16:03 ║
+║ samtools 1.2-4 (arm64) 21 Dec 2015 13:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
-I: NOTICE: Log filtering will replace 'build/samtools-y9iLsV/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-y9iLsV' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-516aafa4-0414-4d26-87f4-6f04e0618260' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-cMi30K/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-cMi30K' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-2faeabd1-88d2-44d2-8613-01450675fd28' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror.bytemark.co.uk unstable InRelease [253 kB]
-Get:2 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:3 http://ftp.debian.org unstable InRelease [253 kB]
-Get:4 http://incoming.debian.org buildd-unstable/main Sources [341 kB]
-Get:5 http://mirror.bytemark.co.uk unstable/main Sources [8093 kB]
-Get:6 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:7 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
-Get:8 http://incoming.debian.org buildd-unstable/main arm64 Packages [96.8 kB]
-Get:9 http://incoming.debian.org buildd-unstable/contrib arm64 Packages [1052 B]
-Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:11 http://mirror.bytemark.co.uk unstable/contrib Sources [59.7 kB]
-Get:12 http://mirror.bytemark.co.uk unstable/non-free Sources [106 kB]
-Get:13 http://mirror.bytemark.co.uk unstable/main arm64 Packages [7240 kB]
-Get:14 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:15 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:16 http://ftp.debian.org unstable/main arm64 Packages [7240 kB]
-Get:17 http://mirror.bytemark.co.uk unstable/contrib arm64 Packages [43.2 kB]
-Get:18 http://ftp.debian.org unstable/contrib arm64 Packages [43.2 kB]
-Fetched 32.1 MB in 9s (3342 kB/s)
+Get:1 http://mirror.bytemark.co.uk/debian unstable InRelease [265 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:3 http://mirror.bytemark.co.uk/debian unstable/main Sources [8421 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:6 http://mirror.bytemark.co.uk/debian unstable/contrib Sources [61.8 kB]
+Get:7 http://mirror.bytemark.co.uk/debian unstable/non-free Sources [105 kB]
+Get:8 http://mirror.bytemark.co.uk/debian unstable/main arm64 Packages [7672 kB]
+Get:9 http://mirror.bytemark.co.uk/debian unstable/contrib arm64 Packages [47.5 kB]
+Get:10 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:11 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:12 http://ftp.debian.org/debian unstable/main arm64 Packages [7672 kB]
+Get:13 http://ftp.debian.org/debian unstable/contrib arm64 Packages [47.5 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [203 kB]
+Get:15 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:16 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:17 http://incoming.debian.org/debian-buildd buildd-unstable/main arm64 Packages [184 kB]
+Get:18 http://incoming.debian.org/debian-buildd buildd-unstable/contrib arm64 Packages [568 B]
+Fetched 33.6 MB in 4s (7692 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 0s (16.0 MB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 1s (2783 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-8B3d39/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-oA1tFt/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]
+Get:1 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ Packages [526 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
-Need to get 0 B/772 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
+Need to get 0 B/770 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-oA1tFt/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+debconf: delaying package configuration, since apt-utils is not installed
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%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11753 files and directories currently installed.)
+(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 ... 12165 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-Az_CnA/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-FbKrJU/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]
+Get:1 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ Packages [734 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 17.5 MB/17.5 MB of archives.
-After this operation, 63.8 MB of additional disk space will be used.
-Get:1 http://mirror.bytemark.co.uk/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://mirror.bytemark.co.uk/debian/ unstable/main groff-base arm64 1.22.3-1 [1166 kB]
-Get:3 http://mirror.bytemark.co.uk/debian/ unstable/main bsdmainutils arm64 9.0.6 [179 kB]
-Get:4 http://mirror.bytemark.co.uk/debian/ unstable/main libpipeline1 arm64 1.4.1-1 [24.8 kB]
-Get:5 http://mirror.bytemark.co.uk/debian/ unstable/main man-db arm64 2.7.3-1 [975 kB]
-Get:6 http://mirror.bytemark.co.uk/debian/ unstable/main libffi6 arm64 3.2.1-3 [18.7 kB]
-Get:7 http://mirror.bytemark.co.uk/debian/ unstable/main libglib2.0-0 arm64 2.44.1-1.1 [2266 kB]
-Get:8 http://mirror.bytemark.co.uk/debian/ unstable/main libicu55 arm64 55.1-5 [7487 kB]
-Get:9 http://mirror.bytemark.co.uk/debian/ unstable/main libxml2 arm64 2.9.2+zdfsg1-4 [781 kB]
-Get:10 http://mirror.bytemark.co.uk/debian/ unstable/main libcroco3 arm64 0.6.8-3+b1 [120 kB]
-Get:11 http://mirror.bytemark.co.uk/debian/ unstable/main libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
-Get:12 http://mirror.bytemark.co.uk/debian/ unstable/main libmagic1 arm64 1:5.25-1 [248 kB]
-Get:13 http://mirror.bytemark.co.uk/debian/ unstable/main file arm64 1:5.25-1 [61.5 kB]
-Get:14 http://mirror.bytemark.co.uk/debian/ unstable/main gettext-base arm64 0.19.6-1 [120 kB]
-Get:15 http://mirror.bytemark.co.uk/debian/ unstable/main gettext arm64 0.19.6-1 [1406 kB]
-Get:16 http://mirror.bytemark.co.uk/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://mirror.bytemark.co.uk/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://mirror.bytemark.co.uk/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://mirror.bytemark.co.uk/debian/ unstable/main libhts1 arm64 1.2.1-1 [191 kB]
-Get:20 http://mirror.bytemark.co.uk/debian/ unstable/main libhts-dev arm64 1.2.1-1 [249 kB]
-Get:21 http://mirror.bytemark.co.uk/debian/ unstable/main libio-pty-perl arm64 1:1.08-1+b1 [34.5 kB]
-Get:22 http://mirror.bytemark.co.uk/debian/ unstable/main libtinfo-dev arm64 6.0+20150810-1 [71.4 kB]
-Get:23 http://mirror.bytemark.co.uk/debian/ unstable/main libncurses5-dev arm64 6.0+20150810-1 [160 kB]
-Get:24 http://mirror.bytemark.co.uk/debian/ unstable/main tabix arm64 1.2.1-1 [186 kB]
-Get:25 http://mirror.bytemark.co.uk/debian/ unstable/main zlib1g-dev arm64 1:1.2.8.dfsg-2+b1 [200 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 5 not upgraded.
+Need to get 17.8 MB/17.8 MB of archives.
+After this operation, 64.7 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-FbKrJU/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [976 B]
+Get:2 http://mirror.bytemark.co.uk/debian unstable/main arm64 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://mirror.bytemark.co.uk/debian unstable/main arm64 groff-base arm64 1.22.3-4 [1155 kB]
+Get:4 http://mirror.bytemark.co.uk/debian unstable/main arm64 bsdmainutils arm64 9.0.6+b1 [178 kB]
+Get:5 http://mirror.bytemark.co.uk/debian unstable/main arm64 libpipeline1 arm64 1.4.1-1 [24.8 kB]
+Get:6 http://mirror.bytemark.co.uk/debian unstable/main arm64 man-db arm64 2.7.5-1 [975 kB]
+Get:7 http://mirror.bytemark.co.uk/debian unstable/main arm64 libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
+Get:8 http://mirror.bytemark.co.uk/debian unstable/main arm64 libmagic1 arm64 1:5.25-2 [248 kB]
+Get:9 http://mirror.bytemark.co.uk/debian unstable/main arm64 file arm64 1:5.25-2 [61.5 kB]
+Get:10 http://mirror.bytemark.co.uk/debian unstable/main arm64 gettext-base arm64 0.19.6-1 [120 kB]
+Get:11 http://mirror.bytemark.co.uk/debian unstable/main arm64 libicu55 arm64 55.1-6 [7491 kB]
+Get:12 http://mirror.bytemark.co.uk/debian unstable/main arm64 libxml2 arm64 2.9.3+dfsg1-1 [785 kB]
+Get:13 http://mirror.bytemark.co.uk/debian unstable/main arm64 libffi6 arm64 3.2.1-4 [18.9 kB]
+Get:14 http://mirror.bytemark.co.uk/debian unstable/main arm64 libglib2.0-0 arm64 2.46.2-1 [2450 kB]
+Get:15 http://mirror.bytemark.co.uk/debian unstable/main arm64 libcroco3 arm64 0.6.11-1 [128 kB]
+Get:16 http://mirror.bytemark.co.uk/debian unstable/main arm64 gettext arm64 0.19.6-1 [1406 kB]
+Get:17 http://mirror.bytemark.co.uk/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://mirror.bytemark.co.uk/debian unstable/main arm64 po-debconf all 1.0.18 [248 kB]
+Get:19 http://mirror.bytemark.co.uk/debian unstable/main arm64 libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://mirror.bytemark.co.uk/debian unstable/main arm64 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://mirror.bytemark.co.uk/debian unstable/main arm64 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://mirror.bytemark.co.uk/debian unstable/main arm64 debhelper all 9.20151220 [830 kB]
+Get:24 http://mirror.bytemark.co.uk/debian unstable/main arm64 libhts1 arm64 1.2.1-2 [191 kB]
+Get:25 http://mirror.bytemark.co.uk/debian unstable/main arm64 libhts-dev arm64 1.2.1-2 [251 kB]
+Get:26 http://mirror.bytemark.co.uk/debian unstable/main arm64 libio-pty-perl arm64 1:1.08-1.1+b1 [32.3 kB]
+Get:27 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtinfo-dev arm64 6.0+20151024-2 [71.3 kB]
+Get:28 http://mirror.bytemark.co.uk/debian unstable/main arm64 libncurses5-dev arm64 6.0+20151024-2 [163 kB]
+Get:29 http://mirror.bytemark.co.uk/debian unstable/main arm64 tabix arm64 1.2.1-2 [187 kB]
+Get:30 http://mirror.bytemark.co.uk/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.8.dfsg-2+b1 [200 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.5 MB in 1s (14.6 MB/s)
+Fetched 17.8 MB in 0s (33.4 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 65%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11753 files and directories currently installed.)
+(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 ... 12165 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_arm64.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_arm64.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_arm64.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_arm64.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../libpipeline1_1.4.1-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_arm64.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:arm64.
-Preparing to unpack .../libffi6_3.2.1-3_arm64.deb ...
-Unpacking libffi6:arm64 (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:arm64.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_arm64.deb ...
-Unpacking libglib2.0-0:arm64 (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:arm64.
-Preparing to unpack .../libicu55_55.1-5_arm64.deb ...
-Unpacking libicu55:arm64 (55.1-5) ...
-Selecting previously unselected package libxml2:arm64.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_arm64.deb ...
-Unpacking libxml2:arm64 (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:arm64.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_arm64.deb ...
-Unpacking libcroco3:arm64 (0.6.8-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_arm64.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:arm64.
Preparing to unpack .../libunistring0_0.9.3-5.2+b2_arm64.deb ...
Unpacking libunistring0:arm64 (0.9.3-5.2+b2) ...
Selecting previously unselected package libmagic1:arm64.
-Preparing to unpack .../libmagic1_1%3a5.25-1_arm64.deb ...
-Unpacking libmagic1:arm64 (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_arm64.deb ...
+Unpacking libmagic1:arm64 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_arm64.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_arm64.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_arm64.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:arm64.
+Preparing to unpack .../libicu55_55.1-6_arm64.deb ...
+Unpacking libicu55:arm64 (55.1-6) ...
+Selecting previously unselected package libxml2:arm64.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_arm64.deb ...
+Unpacking libxml2:arm64 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:arm64.
+Preparing to unpack .../libffi6_3.2.1-4_arm64.deb ...
+Unpacking libffi6:arm64 (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:arm64.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_arm64.deb ...
+Unpacking libglib2.0-0:arm64 (2.46.2-1) ...
+Selecting previously unselected package libcroco3:arm64.
+Preparing to unpack .../libcroco3_0.6.11-1_arm64.deb ...
+Unpacking libcroco3:arm64 (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_arm64.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:arm64.
-Preparing to unpack .../libhts1_1.2.1-1_arm64.deb ...
-Unpacking libhts1:arm64 (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_arm64.deb ...
+Unpacking libhts1:arm64 (1.2.1-2) ...
Selecting previously unselected package libhts-dev:arm64.
-Preparing to unpack .../libhts-dev_1.2.1-1_arm64.deb ...
-Unpacking libhts-dev:arm64 (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_arm64.deb ...
+Unpacking libhts-dev:arm64 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b1_arm64.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b1) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_arm64.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:arm64.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_arm64.deb ...
-Unpacking libtinfo-dev:arm64 (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_arm64.deb ...
+Unpacking libtinfo-dev:arm64 (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:arm64.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_arm64.deb ...
-Unpacking libncurses5-dev:arm64 (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_arm64.deb ...
+Unpacking libncurses5-dev:arm64 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_arm64.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_arm64.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:arm64.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_arm64.deb ...
Unpacking zlib1g-dev:arm64 (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:arm64 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:arm64 (3.2.1-3) ...
-Setting up libglib2.0-0:arm64 (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:arm64 (55.1-5) ...
-Setting up libxml2:arm64 (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:arm64 (0.6.8-3+b1) ...
Setting up libunistring0:arm64 (0.9.3-5.2+b2) ...
-Setting up libmagic1:arm64 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:arm64 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:arm64 (55.1-6) ...
+Setting up libxml2:arm64 (2.9.3+dfsg1-1) ...
+Setting up libffi6:arm64 (3.2.1-4) ...
+Setting up libglib2.0-0:arm64 (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:arm64 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:arm64 (1.2.1-1) ...
-Setting up libhts-dev:arm64 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b1) ...
-Setting up libtinfo-dev:arm64 (6.0+20150810-1) ...
-Setting up libncurses5-dev:arm64 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:arm64 (1.2.1-2) ...
+Setting up libhts-dev:arm64 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:arm64 (6.0+20151024-2) ...
+Setting up libncurses5-dev:arm64 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-arm64 arm64 (aarch64)
-Toolchain package versions: binutils_2.25.1-1 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_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 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+b3 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b3 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b3 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -326,17 +371,19 @@ SCHROOT_CHROOT_NAME=sid-arm64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-arm64-sbuild-516aafa4-0414-4d26-87f4-6f04e0618260
+SCHROOT_SESSION_ID=sid-arm64-sbuild-2faeabd1-88d2-44d2-8613-01450675fd28
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=c8678
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture arm64
@@ -474,82 +521,82 @@ dh_auto_test -- \
make -j6 test HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-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/9A0dTCZs8w/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/NsJx1DyDO8/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/9A0dTCZs8w/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NsJx1DyDO8/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/9A0dTCZs8w/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NsJx1DyDO8/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/9A0dTCZs8w/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/NsJx1DyDO8/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/9A0dTCZs8w/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/NsJx1DyDO8/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/9A0dTCZs8w/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/NsJx1DyDO8/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/9A0dTCZs8w/mpileup.bam.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/NsJx1DyDO8/mpileup.bam.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9A0dTCZs8w/mpileup.bam.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/NsJx1DyDO8/mpileup.bam.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/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/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/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/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/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/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/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/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9A0dTCZs8w/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NsJx1DyDO8/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9A0dTCZs8w/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NsJx1DyDO8/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +826,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.test067.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NsJx1DyDO8/view.test067.sam -h -l Library 2 /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.test069.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NsJx1DyDO8/view.test069.sam -h -l Library 2 /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.test071.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NsJx1DyDO8/view.test071.sam -h -l Library 2 /tmp/NsJx1DyDO8/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/9A0dTCZs8w/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NsJx1DyDO8/view.test006.cram
.. expected failure
@@ -1299,82 +1346,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/9A0dTCZs8w/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/NsJx1DyDO8/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/9A0dTCZs8w/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/NsJx1DyDO8/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/9A0dTCZs8w/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/NsJx1DyDO8/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/9A0dTCZs8w/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/NsJx1DyDO8/depad.001p.bam
.. expected failure
@@ -1412,7 +1459,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/pBv3PCkKtv - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/hRK7Uk3K8T - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1506,6 +1553,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1518,17 +1568,30 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1536,31 +1599,68 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/aarch64-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/lib/aarch64-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/a8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/a8/3f4a655326799efb0ceba1306789dcc72a22b9.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/a8/3f4a655326799efb0ceba1306789dcc72a22b9.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/a8/3f4a655326799efb0ceba1306789dcc72a22b9.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/76
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/76/18af418414c48c0c7e0da7b7ab51b9ba55b54b.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/76/18af418414c48c0c7e0da7b7ab51b9ba55b54b.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/76/18af418414c48c0c7e0da7b7ab51b9ba55b54b.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/45be708a5d368f4dce02ddc538510e5dff25af.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/45be708a5d368f4dce02ddc538510e5dff25af.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/45be708a5d368f4dce02ddc538510e5dff25af.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/e6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/e6/6d6591d8f15358bcad7b0f8ff1ca1ffa7cb1ff.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/e6/6d6591d8f15358bcad7b0f8ff1ca1ffa7cb1ff.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/e6/6d6591d8f15358bcad7b0f8ff1ca1ffa7cb1ff.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/86
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/86/2fa05f90d62952af8306e327aa553b8cead28e.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/86/2fa05f90d62952af8306e327aa553b8cead28e.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/86/2fa05f90d62952af8306e327aa553b8cead28e.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/bc39a532a96e30b9524b7e012f41e1948cc62c.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/bc39a532a96e30b9524b7e012f41e1948cc62c.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/bc39a532a96e30b9524b7e012f41e1948cc62c.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/21
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/21/789220bf027ebfa09af1101bace542051c024b.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/21/789220bf027ebfa09af1101bace542051c024b.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/21/789220bf027ebfa09af1101bace542051c024b.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against ld-linux-aarch64.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=21789220bf027ebfa09af1101bace542051c024b 7145be708a5d368f4dce02ddc538510e5dff25af 7618af418414c48c0c7e0da7b7ab51b9ba [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1570,16 +1670,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_arm64.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_arm64.deb'.
- dpkg-genchanges -B -marm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org> >../samtools_1.2-3_arm64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_arm64.deb'.
+ dpkg-genchanges -B -marm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org> >../samtools_1.2-4_arm64.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1615
+Build finished at 20151221-1329
Finished
────────
@@ -1596,54 +1702,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_arm64.changes:
+samtools_1.2-4_arm64.changes:
─────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: arm64
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
Maintainer: arm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- f0055fe5ae88f389a16280028ab27c84af91e2c5 347256 samtools_1.2-3_arm64.deb
+ d6163cc7e664c4c9bdefa5069d0232abbbc2d88f 416002 samtools-dbgsym_1.2-4_arm64.deb
+ b91ef152719eb861b128151fcb9b5ebee13529ca 349244 samtools_1.2-4_arm64.deb
Checksums-Sha256:
- 82a56ba46b0a2f5dd2bb75dd2d068d2266e9293ac1a76ac60108a90ddd4abbfb 347256 samtools_1.2-3_arm64.deb
+ 58ac5d3ad541b490b2e1e55a6bc89418ea870129603fbe55f1dec5d8ee71a5f7 416002 samtools-dbgsym_1.2-4_arm64.deb
+ c55f1142a75b3c4dd185e4a4298f23dbb68cb7ed0569012a0a2eed1868317328 349244 samtools_1.2-4_arm64.deb
Files:
- 8eb0693afe625864b624591d015d3573 347256 science optional samtools_1.2-3_arm64.deb
+ 47fa75913c4cda3f9689e559c79a4549 416002 debug extra samtools-dbgsym_1.2-4_arm64.deb
+ fdcd20a56bb1340bb7bd04ff7a9bf38c 349244 science optional samtools_1.2-4_arm64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_arm64.deb
+samtools-dbgsym_1.2-4_arm64.deb
+───────────────────────────────
+
+ new debian package, version 2.0.
+ size 416002 bytes: control archive=813 bytes.
+ 646 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: arm64
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 521
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 21789220bf027ebfa09af1101bace542051c024b 7145be708a5d368f4dce02ddc538510e5dff25af 7618af418414c48c0c7e0da7b7ab51b9ba55b54b 862fa05f90d62952af8306e327aa553b8cead28e a83f4a655326799efb0ceba1306789dcc72a22b9 b8bc39a532a96e30b9524b7e012f41e1948cc62c e66d6591d8f15358bcad7b0f8ff1ca1ffa7cb1ff
+
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/21/
+-rw-r--r-- root/root 417512 2015-12-21 13:29 ./usr/lib/debug/.build-id/21/789220bf027ebfa09af1101bace542051c024b.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/71/
+-rw-r--r-- root/root 15560 2015-12-21 13:29 ./usr/lib/debug/.build-id/71/45be708a5d368f4dce02ddc538510e5dff25af.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/76/
+-rw-r--r-- root/root 12728 2015-12-21 13:29 ./usr/lib/debug/.build-id/76/18af418414c48c0c7e0da7b7ab51b9ba55b54b.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/86/
+-rw-r--r-- root/root 13272 2015-12-21 13:29 ./usr/lib/debug/.build-id/86/2fa05f90d62952af8306e327aa553b8cead28e.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/a8/
+-rw-r--r-- root/root 21344 2015-12-21 13:29 ./usr/lib/debug/.build-id/a8/3f4a655326799efb0ceba1306789dcc72a22b9.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/b8/
+-rw-r--r-- root/root 21432 2015-12-21 13:29 ./usr/lib/debug/.build-id/b8/bc39a532a96e30b9524b7e012f41e1948cc62c.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/lib/debug/.build-id/e6/
+-rw-r--r-- root/root 13248 2015-12-21 13:29 ./usr/lib/debug/.build-id/e6/6d6591d8f15358bcad7b0f8ff1ca1ffa7cb1ff.debug
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 13:29 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_arm64.deb
────────────────────────
new debian package, version 2.0.
- size 347256 bytes: control archive=1484 bytes.
- 802 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 349244 bytes: control archive=1607 bytes.
+ 807 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 957
+ Installed-Size: 960
Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1653,44 +1812,51 @@ samtools_1.2-3_arm64.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 16:15 ./
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/bin/
--rwxr-xr-x root/root 18480 2015-09-22 16:15 ./usr/bin/ace2sam
+ one 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 2015-12-21 13:29 ./
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/bin/
+-rwxr-xr-x root/root 18608 2015-12-21 13:29 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 10256 2015-09-22 16:15 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10256 2015-09-22 16:15 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14352 2015-09-22 16:15 ./usr/bin/md5fa
--rwxr-xr-x root/root 10200 2015-09-22 16:15 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 10392 2015-12-21 13:29 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10392 2015-12-21 13:29 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14480 2015-12-21 13:29 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10328 2015-12-21 13:29 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 695776 2015-09-22 16:15 ./usr/bin/samtools
+-rwxr-xr-x root/root 691808 2015-12-21 13:29 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 26760 2015-09-22 16:15 ./usr/bin/wgsim
+-rwxr-xr-x root/root 26888 2015-12-21 13:29 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 16:15 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 13:29 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 13:29 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 13:29 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 13:29 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 13:29 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1710,23 +1876,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: arm64
-Build-Space: 15120
-Build-Time: 718
+Build-Space: 16068
+Build-Time: 685
Distribution: sid
Host Architecture: arm64
-Install-Time: 13
-Job: samtools_1.2-3
+Install-Time: 17
+Job: samtools_1.2-4
Machine Architecture: arm64
Package: samtools
-Package-Time: 755
-Source-Version: 1.2-3
-Space: 15120
+Package-Time: 724
+Source-Version: 1.2-4
+Space: 16068
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1615
-Build needed 00:12:35, 15120k disc space
+Finished at 20151221-1329
+Build needed 00:12:04, 16068k disc space
Signature with key 'FD6F04EA' requested:
- signfile /home/buildd/build/samtools_1.2-3_arm64.changes FD6F04EA
+ signfile /home/buildd/build/samtools_1.2-4_arm64.changes FD6F04EA
Successfully signed changes file
diff --git a/armel.log b/armel.log
index 14c408a..6c39805 100644
--- a/armel.log
+++ b/armel.log
@@ -1,46 +1,47 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on antheil.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arnold.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (armel) 22 Sep 2015 16:17 ║
+║ samtools 1.2-4 (armel) 21 Dec 2015 17:43 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: armel
Host Architecture: armel
Build Architecture: armel
-I: NOTICE: Log filtering will replace 'build/samtools-gPwsTX/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-gPwsTX' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-armel-sbuild-f32f02fb-b239-4cfc-bdbc-eb43798d193b' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-vLTAV4/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-vLTAV4' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-armel-sbuild-c2aa3adc-a9a5-4aad-b663-b5ed5764a2bf' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.uk.debian.org unstable InRelease [253 kB]
-Get:2 http://ftp.debian.org unstable InRelease [253 kB]
-Get:3 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:5 http://ftp.uk.debian.org unstable/main Sources [8093 kB]
-Get:6 http://incoming.debian.org buildd-unstable/main Sources [354 kB]
-Get:7 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:8 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:9 http://ftp.debian.org unstable/main armel Packages [7409 kB]
-Get:10 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:11 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
-Get:12 http://ftp.debian.org unstable/contrib armel Packages [45.2 kB]
-Get:13 http://incoming.debian.org buildd-unstable/main armel Packages [101 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib armel Packages [1056 B]
-Get:15 http://ftp.uk.debian.org unstable/contrib Sources [59.7 kB]
-Get:16 http://ftp.uk.debian.org unstable/non-free Sources [106 kB]
-Get:17 http://ftp.uk.debian.org unstable/main armel Packages [7409 kB]
-Get:18 http://ftp.uk.debian.org unstable/contrib armel Packages [45.2 kB]
-Fetched 32.5 MB in 32s (988 kB/s)
+Get:1 http://mirror.bytemark.co.uk/debian unstable InRelease [265 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://mirror.bytemark.co.uk/debian unstable/main Sources [8422 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [205 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main armel Packages [172 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib armel Packages [568 B]
+Get:10 http://mirror.bytemark.co.uk/debian unstable/contrib Sources [61.8 kB]
+Get:11 http://mirror.bytemark.co.uk/debian unstable/non-free Sources [105 kB]
+Get:12 http://mirror.bytemark.co.uk/debian unstable/main armel Packages [7523 kB]
+Get:13 http://ftp.debian.org/debian unstable/main Sources [8422 kB]
+Get:14 http://mirror.bytemark.co.uk/debian unstable/contrib armel Packages [47.5 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:17 http://ftp.debian.org/debian unstable/main armel Packages [7523 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib armel Packages [47.5 kB]
+Fetched 33.3 MB in 9s (3682 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 8s (533 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://mirror.bytemark.co.uk/debian unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://mirror.bytemark.co.uk/debian unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://mirror.bytemark.co.uk/debian unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 0s (8838 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-2tF7AU/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-T8WOr9/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]
+Get:1 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ Packages [526 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 0 B/774 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-T8WOr9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
+debconf: delaying package configuration, since apt-utils is not installed
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 ... 11623 files and directories currently installed.)
+(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 ... 12037 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-uP4prh/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-1IfftF/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]
+Get:1 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ Packages [729 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 17.3 MB/17.3 MB of archives.
-After this operation, 64.3 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.22.3-1 [1123 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.6 [178 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.4.1-1 [23.5 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.7.3-1 [977 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi6 armel 3.2.1-3 [18.3 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.44.1-1.1 [2312 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libicu55 armel 55.1-5 [7341 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.9.2+zdfsg1-4 [801 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.8-3+b1 [124 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5.2+b1 [253 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 1:5.25-1 [251 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main file armel 1:5.25-1 [61.1 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.19.6-1 [119 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.19.6-1 [1399 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libhts1 armel 1.2.1-1 [193 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev armel 1.2.1-1 [241 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main libio-pty-perl armel 1:1.08-1+b4 [35.2 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 6.0+20150810-1 [66.4 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 6.0+20150810-1 [155 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main tabix armel 1.2.1-1 [183 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.8.dfsg-2+b1 [200 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 1 not upgraded.
+Need to get 17.7 MB/17.7 MB of archives.
+After this operation, 64.9 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-1IfftF/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [980 B]
+Get:2 http://mirror.bytemark.co.uk/debian unstable/main armel bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://mirror.bytemark.co.uk/debian unstable/main armel groff-base armel 1.22.3-4 [1099 kB]
+Get:4 http://mirror.bytemark.co.uk/debian unstable/main armel bsdmainutils armel 9.0.6+b1 [178 kB]
+Get:5 http://mirror.bytemark.co.uk/debian unstable/main armel libpipeline1 armel 1.4.1-1 [23.5 kB]
+Get:6 http://mirror.bytemark.co.uk/debian unstable/main armel man-db armel 2.7.5-1 [977 kB]
+Get:7 http://mirror.bytemark.co.uk/debian unstable/main armel libunistring0 armel 0.9.3-5.2+b1 [253 kB]
+Get:8 http://mirror.bytemark.co.uk/debian unstable/main armel libmagic1 armel 1:5.25-2 [252 kB]
+Get:9 http://mirror.bytemark.co.uk/debian unstable/main armel file armel 1:5.25-2 [61.1 kB]
+Get:10 http://mirror.bytemark.co.uk/debian unstable/main armel gettext-base armel 0.19.6-1 [119 kB]
+Get:11 http://mirror.bytemark.co.uk/debian unstable/main armel libicu55 armel 55.1-6 [7343 kB]
+Get:12 http://mirror.bytemark.co.uk/debian unstable/main armel libxml2 armel 2.9.3+dfsg1-1 [803 kB]
+Get:13 http://mirror.bytemark.co.uk/debian unstable/main armel libffi6 armel 3.2.1-4 [18.5 kB]
+Get:14 http://mirror.bytemark.co.uk/debian unstable/main armel libglib2.0-0 armel 2.46.2-1 [2486 kB]
+Get:15 http://mirror.bytemark.co.uk/debian unstable/main armel libcroco3 armel 0.6.11-1 [132 kB]
+Get:16 http://mirror.bytemark.co.uk/debian unstable/main armel gettext armel 0.19.6-1 [1399 kB]
+Get:17 http://mirror.bytemark.co.uk/debian unstable/main armel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://mirror.bytemark.co.uk/debian unstable/main armel po-debconf all 1.0.18 [248 kB]
+Get:19 http://mirror.bytemark.co.uk/debian unstable/main armel libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://mirror.bytemark.co.uk/debian unstable/main armel libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://mirror.bytemark.co.uk/debian unstable/main armel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://mirror.bytemark.co.uk/debian unstable/main armel dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://mirror.bytemark.co.uk/debian unstable/main armel debhelper all 9.20151220 [830 kB]
+Get:24 http://mirror.bytemark.co.uk/debian unstable/main armel libhts1 armel 1.2.1-2 [192 kB]
+Get:25 http://mirror.bytemark.co.uk/debian unstable/main armel libhts-dev armel 1.2.1-2 [241 kB]
+Get:26 http://mirror.bytemark.co.uk/debian unstable/main armel libio-pty-perl armel 1:1.08-1.1+b1 [33.2 kB]
+Get:27 http://mirror.bytemark.co.uk/debian unstable/main armel libtinfo-dev armel 6.0+20151024-2 [66.4 kB]
+Get:28 http://mirror.bytemark.co.uk/debian unstable/main armel libncurses5-dev armel 6.0+20151024-2 [158 kB]
+Get:29 http://mirror.bytemark.co.uk/debian unstable/main armel tabix armel 1.2.1-2 [183 kB]
+Get:30 http://mirror.bytemark.co.uk/debian unstable/main armel zlib1g-dev armel 1:1.2.8.dfsg-2+b1 [200 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.3 MB in 7s (2209 kB/s)
+Fetched 17.7 MB in 1s (15.6 MB/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 ... 11623 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
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(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 ... 12037 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_armel.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_armel.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_armel.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_armel.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:armel.
Preparing to unpack .../libpipeline1_1.4.1-1_armel.deb ...
Unpacking libpipeline1:armel (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_armel.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:armel.
-Preparing to unpack .../libffi6_3.2.1-3_armel.deb ...
-Unpacking libffi6:armel (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:armel.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_armel.deb ...
-Unpacking libglib2.0-0:armel (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:armel.
-Preparing to unpack .../libicu55_55.1-5_armel.deb ...
-Unpacking libicu55:armel (55.1-5) ...
-Selecting previously unselected package libxml2:armel.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_armel.deb ...
-Unpacking libxml2:armel (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:armel.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_armel.deb ...
-Unpacking libcroco3:armel (0.6.8-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_armel.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:armel.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_armel.deb ...
Unpacking libunistring0:armel (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:armel.
-Preparing to unpack .../libmagic1_1%3a5.25-1_armel.deb ...
-Unpacking libmagic1:armel (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_armel.deb ...
+Unpacking libmagic1:armel (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_armel.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_armel.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_armel.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:armel.
+Preparing to unpack .../libicu55_55.1-6_armel.deb ...
+Unpacking libicu55:armel (55.1-6) ...
+Selecting previously unselected package libxml2:armel.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_armel.deb ...
+Unpacking libxml2:armel (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:armel.
+Preparing to unpack .../libffi6_3.2.1-4_armel.deb ...
+Unpacking libffi6:armel (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:armel.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_armel.deb ...
+Unpacking libglib2.0-0:armel (2.46.2-1) ...
+Selecting previously unselected package libcroco3:armel.
+Preparing to unpack .../libcroco3_0.6.11-1_armel.deb ...
+Unpacking libcroco3:armel (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_armel.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:armel.
-Preparing to unpack .../libhts1_1.2.1-1_armel.deb ...
-Unpacking libhts1:armel (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_armel.deb ...
+Unpacking libhts1:armel (1.2.1-2) ...
Selecting previously unselected package libhts-dev:armel.
-Preparing to unpack .../libhts-dev_1.2.1-1_armel.deb ...
-Unpacking libhts-dev:armel (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_armel.deb ...
+Unpacking libhts-dev:armel (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_armel.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_armel.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:armel.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_armel.deb ...
-Unpacking libtinfo-dev:armel (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_armel.deb ...
+Unpacking libtinfo-dev:armel (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:armel.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_armel.deb ...
-Unpacking libncurses5-dev:armel (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_armel.deb ...
+Unpacking libncurses5-dev:armel (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_armel.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_armel.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:armel.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armel.deb ...
Unpacking zlib1g-dev:armel (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:armel (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:armel (3.2.1-3) ...
-Setting up libglib2.0-0:armel (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:armel (55.1-5) ...
-Setting up libxml2:armel (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:armel (0.6.8-3+b1) ...
Setting up libunistring0:armel (0.9.3-5.2+b1) ...
-Setting up libmagic1:armel (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:armel (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:armel (55.1-6) ...
+Setting up libxml2:armel (2.9.3+dfsg1-1) ...
+Setting up libffi6:armel (3.2.1-4) ...
+Setting up libglib2.0-0:armel (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:armel (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:armel (1.2.1-1) ...
-Setting up libhts-dev:armel (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:armel (6.0+20150810-1) ...
-Setting up libncurses5-dev:armel (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:armel (1.2.1-2) ...
+Setting up libhts-dev:armel (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:armel (6.0+20151024-2) ...
+Setting up libncurses5-dev:armel (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:armel (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-armmp-lpae armel (armv7l)
-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_1:2.27-3 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 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_1.42.13-1 faker [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -326,17 +371,19 @@ SCHROOT_CHROOT_NAME=sid-armel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-armel-sbuild-f32f02fb-b239-4cfc-bdbc-eb43798d193b
+SCHROOT_SESSION_ID=sid-armel-sbuild-c2aa3adc-a9a5-4aad-b663-b5ed5764a2bf
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=c11131
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture armel
@@ -474,82 +521,82 @@ dh_auto_test -- \
make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/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/pUOoPqG2pH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/glz6ctagQ_/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/pUOoPqG2pH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/glz6ctagQ_/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/pUOoPqG2pH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/glz6ctagQ_/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/pUOoPqG2pH/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/glz6ctagQ_/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/pUOoPqG2pH/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/glz6ctagQ_/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/pUOoPqG2pH/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/glz6ctagQ_/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/pUOoPqG2pH/mpileup.bam.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/glz6ctagQ_/mpileup.bam.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pUOoPqG2pH/mpileup.bam.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/glz6ctagQ_/mpileup.bam.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/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/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/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/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/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/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/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/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pUOoPqG2pH/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/glz6ctagQ_/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pUOoPqG2pH/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:1050-1060 /tmp/glz6ctagQ_/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +826,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/glz6ctagQ_/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/glz6ctagQ_/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/glz6ctagQ_/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/glz6ctagQ_/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.test067.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/glz6ctagQ_/view.test067.sam -h -l Library 2 /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.test069.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/glz6ctagQ_/view.test069.sam -h -l Library 2 /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.test071.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/glz6ctagQ_/view.test071.sam -h -l Library 2 /tmp/glz6ctagQ_/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/pUOoPqG2pH/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/glz6ctagQ_/view.test006.cram
.. expected failure
@@ -1299,82 +1346,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/pUOoPqG2pH/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/glz6ctagQ_/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/pUOoPqG2pH/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/glz6ctagQ_/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/pUOoPqG2pH/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/glz6ctagQ_/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/pUOoPqG2pH/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/glz6ctagQ_/depad.001p.bam
.. expected failure
@@ -1412,7 +1459,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/729OaulfUa - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/XquZzCyn01 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1506,6 +1553,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1518,17 +1568,30 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1536,31 +1599,68 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/arm-linux-gnueabi/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/lib/arm-linux-gnueabi/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/0d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/0d/812397077f21ad701c769d271ebc430b4ca2c8.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/0d/812397077f21ad701c769d271ebc430b4ca2c8.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/0d/812397077f21ad701c769d271ebc430b4ca2c8.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/70
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/70/2fb1523b8d0ff036b38f3a68a2e1da8cb16937.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/70/2fb1523b8d0ff036b38f3a68a2e1da8cb16937.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/70/2fb1523b8d0ff036b38f3a68a2e1da8cb16937.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/73
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/73/9eaf496f1e2f0bba2868ae1c5a3be6c9d894ff.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/73/9eaf496f1e2f0bba2868ae1c5a3be6c9d894ff.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/73/9eaf496f1e2f0bba2868ae1c5a3be6c9d894ff.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/4ab39170926f40e1cedcb691e619ad5c18b6a6.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/4ab39170926f40e1cedcb691e619ad5c18b6a6.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/4ab39170926f40e1cedcb691e619ad5c18b6a6.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cb
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cb/cb3cc8a6ce134bb3b74edc73133fd73b530c45.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cb/cb3cc8a6ce134bb3b74edc73133fd73b530c45.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cb/cb3cc8a6ce134bb3b74edc73133fd73b530c45.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/fc5d4c517398d0431e9a1b555a37bfdcbfc7b4.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/fc5d4c517398d0431e9a1b555a37bfdcbfc7b4.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/fc5d4c517398d0431e9a1b555a37bfdcbfc7b4.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/256701231944ec6dfa646bd40db6cc49c0627b.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/256701231944ec6dfa646bd40db6cc49c0627b.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b8/256701231944ec6dfa646bd40db6cc49c0627b.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short were not linked against ld-linux.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=0d812397077f21ad701c769d271ebc430b4ca2c8 4dfc5d4c517398d0431e9a1b555a37bfdcbfc7b4 702fb1523b8d0ff036b38f3a68a2e1da8c [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1570,16 +1670,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_armel.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_armel.deb'.
- dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../samtools_1.2-3_armel.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (arnold) <buildd_armel-arnold at buildd.debian.org> >../samtools_1.2-4_armel.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1632
+Build finished at 20151221-1757
Finished
────────
@@ -1596,54 +1702,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_armel.changes:
+samtools_1.2-4_armel.changes:
─────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: armel
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
-Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Maintainer: armel Build Daemon (arnold) <buildd_armel-arnold at buildd.debian.org>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- 319ccd3f70bf5ea9a2213301128fcc69223b5bc4 336184 samtools_1.2-3_armel.deb
+ fbf95ea98bfcb2677eacad9da0bd0c61cc714749 399216 samtools-dbgsym_1.2-4_armel.deb
+ 30015490b8653c0a1493bae4617f2af57ab7e977 336704 samtools_1.2-4_armel.deb
Checksums-Sha256:
- e30044dd64712620c208ff4c0039b4cf65b760c97b469f88b2ba5f11d57b2171 336184 samtools_1.2-3_armel.deb
+ fef97263a917279c26ec50df9b7fc4468bbd47c11e1927580dd7496637c9f58f 399216 samtools-dbgsym_1.2-4_armel.deb
+ fbe745f379bbeee72f8d9f9cab8a68e021db8dca22513fcff2af3003429b380f 336704 samtools_1.2-4_armel.deb
Files:
- 0558d5438222c9a2c4208ae15337b658 336184 science optional samtools_1.2-3_armel.deb
+ 78d6e0429bb10c10bbe8ab8c6dfb2ba7 399216 debug extra samtools-dbgsym_1.2-4_armel.deb
+ 55c2dad457c9e3de2a3fbceaecb07e49 336704 science optional samtools_1.2-4_armel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_armel.deb
+samtools-dbgsym_1.2-4_armel.deb
+───────────────────────────────
+
+ new debian package, version 2.0.
+ size 399216 bytes: control archive=820 bytes.
+ 646 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: armel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 496
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 0d812397077f21ad701c769d271ebc430b4ca2c8 4dfc5d4c517398d0431e9a1b555a37bfdcbfc7b4 702fb1523b8d0ff036b38f3a68a2e1da8cb16937 739eaf496f1e2f0bba2868ae1c5a3be6c9d894ff 7a4ab39170926f40e1cedcb691e619ad5c18b6a6 b8256701231944ec6dfa646bd40db6cc49c0627b cbcb3cc8a6ce134bb3b74edc73133fd73b530c45
+
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/0d/
+-rw-r--r-- root/root 19376 2015-12-21 17:57 ./usr/lib/debug/.build-id/0d/812397077f21ad701c769d271ebc430b4ca2c8.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/4d/
+-rw-r--r-- root/root 19140 2015-12-21 17:57 ./usr/lib/debug/.build-id/4d/fc5d4c517398d0431e9a1b555a37bfdcbfc7b4.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/70/
+-rw-r--r-- root/root 10960 2015-12-21 17:57 ./usr/lib/debug/.build-id/70/2fb1523b8d0ff036b38f3a68a2e1da8cb16937.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/73/
+-rw-r--r-- root/root 13660 2015-12-21 17:57 ./usr/lib/debug/.build-id/73/9eaf496f1e2f0bba2868ae1c5a3be6c9d894ff.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/7a/
+-rw-r--r-- root/root 11020 2015-12-21 17:57 ./usr/lib/debug/.build-id/7a/4ab39170926f40e1cedcb691e619ad5c18b6a6.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/b8/
+-rw-r--r-- root/root 404032 2015-12-21 17:57 ./usr/lib/debug/.build-id/b8/256701231944ec6dfa646bd40db6cc49c0627b.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/lib/debug/.build-id/cb/
+-rw-r--r-- root/root 11036 2015-12-21 17:57 ./usr/lib/debug/.build-id/cb/cb3cc8a6ce134bb3b74edc73133fd73b530c45.debug
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 17:57 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_armel.deb
────────────────────────
new debian package, version 2.0.
- size 336184 bytes: control archive=1484 bytes.
- 802 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 336704 bytes: control archive=1607 bytes.
+ 807 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: armel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 967
+ Installed-Size: 969
Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1653,44 +1812,51 @@ samtools_1.2-3_armel.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 16:32 ./
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/bin/
--rwxr-xr-x root/root 17864 2015-09-22 16:32 ./usr/bin/ace2sam
+ one 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 2015-12-21 17:57 ./
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/bin/
+-rwxr-xr-x root/root 17972 2015-12-21 17:57 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 9656 2015-09-22 16:32 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 9656 2015-09-22 16:32 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 13752 2015-09-22 16:32 ./usr/bin/md5fa
--rwxr-xr-x root/root 9628 2015-09-22 16:32 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 9768 2015-12-21 17:57 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9768 2015-12-21 17:57 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13860 2015-12-21 17:57 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9736 2015-12-21 17:57 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 715032 2015-09-22 16:32 ./usr/bin/samtools
+-rwxr-xr-x root/root 711044 2015-12-21 17:57 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 22020 2015-09-22 16:32 ./usr/bin/wgsim
+-rwxr-xr-x root/root 22128 2015-12-21 17:57 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 16:32 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 17:57 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 17:57 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 17:57 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 17:57 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 17:57 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1710,23 +1876,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armel
-Build-Space: 14816
-Build-Time: 732
+Build-Space: 15724
+Build-Time: 720
Distribution: sid
Host Architecture: armel
-Install-Time: 40
-Job: samtools_1.2-3
+Install-Time: 39
+Job: samtools_1.2-4
Machine Architecture: armel
Package: samtools
-Package-Time: 896
-Source-Version: 1.2-3
-Space: 14816
+Package-Time: 801
+Source-Version: 1.2-4
+Space: 15724
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1632
-Build needed 00:14:56, 14816k disc space
-Signature with key '08BE2BFD' requested:
- signfile /home/buildd/build/samtools_1.2-3_armel.changes 08BE2BFD
+Finished at 20151221-1757
+Build needed 00:13:21, 15724k disc space
+Signature with key '2AE5FB34' requested:
+ signfile /home/buildd/build/samtools_1.2-4_armel.changes 2AE5FB34
Successfully signed changes file
diff --git a/i386.log b/i386.log
index 6409da5..885124e 100644
--- a/i386.log
+++ b/i386.log
@@ -2,45 +2,46 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-csail-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (i386) 22 Sep 2015 16:06 ║
+║ samtools 1.2-4 (i386) 21 Dec 2015 13:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: amd64
Host Architecture: i386
Build Architecture: i386
-I: NOTICE: Log filtering will replace 'build/samtools-Et2_7Z/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-Et2_7Z' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-1cb31428-a4ec-4cce-8d40-8cfe912fabad' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-QXbpKY/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-QXbpKY' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-15d4cef1-a50f-494f-91b6-346ddafe30b1' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://debian.csail.mit.edu unstable InRelease [253 kB]
-Get:2 http://debian.csail.mit.edu unstable/main Sources [8093 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:4 http://ftp.debian.org unstable InRelease [253 kB]
-Get:5 http://incoming.debian.org buildd-unstable/main Sources [341 kB]
-Get:6 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:7 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
-Get:8 http://incoming.debian.org buildd-unstable/main i386 Packages [99.6 kB]
-Get:9 http://incoming.debian.org buildd-unstable/contrib i386 Packages [1056 B]
-Get:10 http://debian.csail.mit.edu unstable/contrib Sources [59.7 kB]
-Get:11 http://debian.csail.mit.edu unstable/non-free Sources [106 kB]
-Get:12 http://debian.csail.mit.edu unstable/main i386 Packages [7549 kB]
-Get:13 http://debian.csail.mit.edu unstable/contrib i386 Packages [57.8 kB]
-Get:14 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:17 http://ftp.debian.org unstable/main i386 Packages [7549 kB]
-Get:18 http://ftp.debian.org unstable/contrib i386 Packages [57.8 kB]
-Fetched 32.8 MB in 11s (2913 kB/s)
+Get:1 http://debian.csail.mit.edu/debian unstable InRelease [265 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [203 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/main i386 Packages [210 kB]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/contrib i386 Packages [568 B]
+Get:8 http://debian.csail.mit.edu/debian unstable/main Sources [8421 kB]
+Get:9 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:10 http://debian.csail.mit.edu/debian unstable/contrib Sources [61.8 kB]
+Get:11 http://debian.csail.mit.edu/debian unstable/non-free Sources [105 kB]
+Get:12 http://debian.csail.mit.edu/debian unstable/main i386 Packages [7976 kB]
+Get:13 http://debian.csail.mit.edu/debian unstable/contrib i386 Packages [60.9 kB]
+Get:14 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:17 http://ftp.debian.org/debian unstable/main i386 Packages [7976 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib i386 Packages [60.9 kB]
+Fetched 34.3 MB in 4s (6996 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 0s (24.1 MB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 0s (48.8 MB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-A798Xu/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-Kx9D7o/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]
+Get:1 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ Packages [527 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
-Need to get 0 B/774 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
+Need to get 0 B/770 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-Kx9D7o/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+debconf: delaying package configuration, since apt-utils is not installed
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%
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(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 ... 11918 files and directories currently installed.)
+(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 ... 12351 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-Sw8sPU/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-rqXVAe/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]
+Get:1 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ Packages [733 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 18.5 MB/18.5 MB of archives.
-After this operation, 65.2 MB of additional disk space will be used.
-Get:1 http://debian.csail.mit.edu/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://debian.csail.mit.edu/debian/ unstable/main groff-base i386 1.22.3-1 [1174 kB]
-Get:3 http://debian.csail.mit.edu/debian/ unstable/main bsdmainutils i386 9.0.6 [183 kB]
-Get:4 http://debian.csail.mit.edu/debian/ unstable/main libpipeline1 i386 1.4.1-1 [29.8 kB]
-Get:5 http://debian.csail.mit.edu/debian/ unstable/main man-db i386 2.7.3-1 [1011 kB]
-Get:6 http://debian.csail.mit.edu/debian/ unstable/main libffi6 i386 3.2.1-3 [19.2 kB]
-Get:7 http://debian.csail.mit.edu/debian/ unstable/main libglib2.0-0 i386 2.44.1-1.1 [2522 kB]
-Get:8 http://debian.csail.mit.edu/debian/ unstable/main libicu55 i386 55.1-5 [7762 kB]
-Get:9 http://debian.csail.mit.edu/debian/ unstable/main libxml2 i386 2.9.2+zdfsg1-4 [945 kB]
-Get:10 http://debian.csail.mit.edu/debian/ unstable/main libcroco3 i386 0.6.8-3+b1 [141 kB]
-Get:11 http://debian.csail.mit.edu/debian/ unstable/main libunistring0 i386 0.9.3-5.2+b1 [288 kB]
-Get:12 http://debian.csail.mit.edu/debian/ unstable/main libmagic1 i386 1:5.25-1 [261 kB]
-Get:13 http://debian.csail.mit.edu/debian/ unstable/main file i386 1:5.25-1 [61.4 kB]
-Get:14 http://debian.csail.mit.edu/debian/ unstable/main gettext-base i386 0.19.6-1 [123 kB]
-Get:15 http://debian.csail.mit.edu/debian/ unstable/main gettext i386 0.19.6-1 [1473 kB]
-Get:16 http://debian.csail.mit.edu/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://debian.csail.mit.edu/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://debian.csail.mit.edu/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://debian.csail.mit.edu/debian/ unstable/main libhts1 i386 1.2.1-1 [240 kB]
-Get:20 http://debian.csail.mit.edu/debian/ unstable/main libhts-dev i386 1.2.1-1 [283 kB]
-Get:21 http://debian.csail.mit.edu/debian/ unstable/main libio-pty-perl i386 1:1.08-1+b4 [36.4 kB]
-Get:22 http://debian.csail.mit.edu/debian/ unstable/main libtinfo-dev i386 6.0+20150810-1 [76.5 kB]
-Get:23 http://debian.csail.mit.edu/debian/ unstable/main libncurses5-dev i386 6.0+20150810-1 [174 kB]
-Get:24 http://debian.csail.mit.edu/debian/ unstable/main tabix i386 1.2.1-1 [230 kB]
-Get:25 http://debian.csail.mit.edu/debian/ unstable/main zlib1g-dev i386 1:1.2.8.dfsg-2+b1 [205 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 5 not upgraded.
+Need to get 18.9 MB/18.9 MB of archives.
+After this operation, 66.0 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-rqXVAe/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [976 B]
+Get:2 http://debian.csail.mit.edu/debian unstable/main i386 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://debian.csail.mit.edu/debian unstable/main i386 groff-base i386 1.22.3-4 [1192 kB]
+Get:4 http://debian.csail.mit.edu/debian unstable/main i386 bsdmainutils i386 9.0.6+b1 [183 kB]
+Get:5 http://debian.csail.mit.edu/debian unstable/main i386 libpipeline1 i386 1.4.1-1 [29.8 kB]
+Get:6 http://debian.csail.mit.edu/debian unstable/main i386 man-db i386 2.7.5-1 [1011 kB]
+Get:7 http://debian.csail.mit.edu/debian unstable/main i386 libunistring0 i386 0.9.3-5.2+b1 [288 kB]
+Get:8 http://debian.csail.mit.edu/debian unstable/main i386 libmagic1 i386 1:5.25-2 [261 kB]
+Get:9 http://debian.csail.mit.edu/debian unstable/main i386 file i386 1:5.25-2 [61.5 kB]
+Get:10 http://debian.csail.mit.edu/debian unstable/main i386 gettext-base i386 0.19.6-1 [123 kB]
+Get:11 http://debian.csail.mit.edu/debian unstable/main i386 libicu55 i386 55.1-6 [7760 kB]
+Get:12 http://debian.csail.mit.edu/debian unstable/main i386 libxml2 i386 2.9.3+dfsg1-1 [951 kB]
+Get:13 http://debian.csail.mit.edu/debian unstable/main i386 libffi6 i386 3.2.1-4 [19.5 kB]
+Get:14 http://debian.csail.mit.edu/debian unstable/main i386 libglib2.0-0 i386 2.46.2-1 [2707 kB]
+Get:15 http://debian.csail.mit.edu/debian unstable/main i386 libcroco3 i386 0.6.11-1 [149 kB]
+Get:16 http://debian.csail.mit.edu/debian unstable/main i386 gettext i386 0.19.6-1 [1473 kB]
+Get:17 http://debian.csail.mit.edu/debian unstable/main i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://debian.csail.mit.edu/debian unstable/main i386 po-debconf all 1.0.18 [248 kB]
+Get:19 http://debian.csail.mit.edu/debian unstable/main i386 libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://debian.csail.mit.edu/debian unstable/main i386 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://debian.csail.mit.edu/debian unstable/main i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://debian.csail.mit.edu/debian unstable/main i386 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://debian.csail.mit.edu/debian unstable/main i386 debhelper all 9.20151220 [830 kB]
+Get:24 http://debian.csail.mit.edu/debian unstable/main i386 libhts1 i386 1.2.1-2 [244 kB]
+Get:25 http://debian.csail.mit.edu/debian unstable/main i386 libhts-dev i386 1.2.1-2 [283 kB]
+Get:26 http://debian.csail.mit.edu/debian unstable/main i386 libio-pty-perl i386 1:1.08-1.1+b1 [33.8 kB]
+Get:27 http://debian.csail.mit.edu/debian unstable/main i386 libtinfo-dev i386 6.0+20151024-2 [76.6 kB]
+Get:28 http://debian.csail.mit.edu/debian unstable/main i386 libncurses5-dev i386 6.0+20151024-2 [177 kB]
+Get:29 http://debian.csail.mit.edu/debian unstable/main i386 tabix i386 1.2.1-2 [230 kB]
+Get:30 http://debian.csail.mit.edu/debian unstable/main i386 zlib1g-dev i386 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.5 MB in 1s (18.4 MB/s)
+Fetched 18.9 MB in 0s (42.1 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11918 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
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(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 ... 12351 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_i386.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_i386.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_i386.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_i386.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../libpipeline1_1.4.1-1_i386.deb ...
Unpacking libpipeline1:i386 (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_i386.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:i386.
-Preparing to unpack .../libffi6_3.2.1-3_i386.deb ...
-Unpacking libffi6:i386 (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:i386.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_i386.deb ...
-Unpacking libglib2.0-0:i386 (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:i386.
-Preparing to unpack .../libicu55_55.1-5_i386.deb ...
-Unpacking libicu55:i386 (55.1-5) ...
-Selecting previously unselected package libxml2:i386.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_i386.deb ...
-Unpacking libxml2:i386 (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:i386.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_i386.deb ...
-Unpacking libcroco3:i386 (0.6.8-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_i386.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:i386.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_i386.deb ...
Unpacking libunistring0:i386 (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:i386.
-Preparing to unpack .../libmagic1_1%3a5.25-1_i386.deb ...
-Unpacking libmagic1:i386 (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_i386.deb ...
+Unpacking libmagic1:i386 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_i386.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_i386.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_i386.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:i386.
+Preparing to unpack .../libicu55_55.1-6_i386.deb ...
+Unpacking libicu55:i386 (55.1-6) ...
+Selecting previously unselected package libxml2:i386.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_i386.deb ...
+Unpacking libxml2:i386 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:i386.
+Preparing to unpack .../libffi6_3.2.1-4_i386.deb ...
+Unpacking libffi6:i386 (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:i386.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.46.2-1) ...
+Selecting previously unselected package libcroco3:i386.
+Preparing to unpack .../libcroco3_0.6.11-1_i386.deb ...
+Unpacking libcroco3:i386 (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_i386.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:i386.
-Preparing to unpack .../libhts1_1.2.1-1_i386.deb ...
-Unpacking libhts1:i386 (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_i386.deb ...
+Unpacking libhts1:i386 (1.2.1-2) ...
Selecting previously unselected package libhts-dev:i386.
-Preparing to unpack .../libhts-dev_1.2.1-1_i386.deb ...
-Unpacking libhts-dev:i386 (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_i386.deb ...
+Unpacking libhts-dev:i386 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_i386.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:i386.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_i386.deb ...
-Unpacking libtinfo-dev:i386 (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_i386.deb ...
+Unpacking libtinfo-dev:i386 (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:i386.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_i386.deb ...
-Unpacking libncurses5-dev:i386 (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_i386.deb ...
+Unpacking libncurses5-dev:i386 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_i386.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_i386.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:i386.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_i386.deb ...
Unpacking zlib1g-dev:i386 (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:i386 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:i386 (3.2.1-3) ...
-Setting up libglib2.0-0:i386 (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:i386 (55.1-5) ...
-Setting up libxml2:i386 (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:i386 (0.6.8-3+b1) ...
Setting up libunistring0:i386 (0.9.3-5.2+b1) ...
-Setting up libmagic1:i386 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:i386 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:i386 (55.1-6) ...
+Setting up libxml2:i386 (2.9.3+dfsg1-1) ...
+Setting up libffi6:i386 (3.2.1-4) ...
+Setting up libglib2.0-0:i386 (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:i386 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:i386 (1.2.1-1) ...
-Setting up libhts-dev:i386 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:i386 (6.0+20150810-1) ...
-Setting up libncurses5-dev:i386 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:i386 (1.2.1-2) ...
+Setting up libhts-dev:i386 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:i386 (6.0+20151024-2) ...
+Setting up libncurses5-dev:i386 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.25.1-1 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_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 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 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_1.42.13-1 faker [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -326,17 +371,19 @@ SCHROOT_CHROOT_NAME=sid-i386-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-i386-sbuild-1cb31428-a4ec-4cce-8d40-8cfe912fabad
+SCHROOT_SESSION_ID=sid-i386-sbuild-15d4cef1-a50f-494f-91b6-346ddafe30b1
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture i386
@@ -474,82 +521,82 @@ dh_auto_test -- \
make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-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/drlgpH3C_c/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/8wT_XD_FtD/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/drlgpH3C_c/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/8wT_XD_FtD/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/drlgpH3C_c/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/8wT_XD_FtD/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/drlgpH3C_c/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/8wT_XD_FtD/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/drlgpH3C_c/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/8wT_XD_FtD/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/drlgpH3C_c/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/8wT_XD_FtD/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/drlgpH3C_c/mpileup.bam.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/8wT_XD_FtD/mpileup.bam.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/drlgpH3C_c/mpileup.bam.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/8wT_XD_FtD/mpileup.bam.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/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/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/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/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/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/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/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/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:1050-1060 /tmp/drlgpH3C_c/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8wT_XD_FtD/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:1050-1060 /tmp/drlgpH3C_c/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:1050-1060 /tmp/8wT_XD_FtD/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +826,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/drlgpH3C_c/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/drlgpH3C_c/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/drlgpH3C_c/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/drlgpH3C_c/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.test067.sam -h -l Library 2 /tmp/drlgpH3C_c/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/8wT_XD_FtD/view.test067.sam -h -l Library 2 /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.test069.sam -h -l Library 2 /tmp/drlgpH3C_c/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/8wT_XD_FtD/view.test069.sam -h -l Library 2 /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.test071.sam -h -l Library 2 /tmp/drlgpH3C_c/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/8wT_XD_FtD/view.test071.sam -h -l Library 2 /tmp/8wT_XD_FtD/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/drlgpH3C_c/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/8wT_XD_FtD/view.test006.cram
.. expected failure
@@ -1299,82 +1346,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/drlgpH3C_c/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/8wT_XD_FtD/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/drlgpH3C_c/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/8wT_XD_FtD/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/drlgpH3C_c/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/8wT_XD_FtD/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/drlgpH3C_c/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/8wT_XD_FtD/depad.001p.bam
.. expected failure
@@ -1412,7 +1459,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/LYZcGZxZrg - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/dCWbBNXYIG - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1506,6 +1553,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1518,17 +1568,30 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1536,31 +1599,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/i386-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/lib/i386-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b9/edc7147ae8f6f460e1369e71c4c7dfca62ec9d.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b9/edc7147ae8f6f460e1369e71c4c7dfca62ec9d.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b9/edc7147ae8f6f460e1369e71c4c7dfca62ec9d.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/4835c46354336bbcf9e71ddf24eeed56ab6a3d.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/4835c46354336bbcf9e71ddf24eeed56ab6a3d.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/71/4835c46354336bbcf9e71ddf24eeed56ab6a3d.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/61
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/61/a9dfbfe3cde373f3a3b42c89a28190907e3cfd.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/61/a9dfbfe3cde373f3a3b42c89a28190907e3cfd.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/61/a9dfbfe3cde373f3a3b42c89a28190907e3cfd.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fa
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fa/e4ada1a57cc57f33d1fcf57b0f2c3d77bf4a96.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fa/e4ada1a57cc57f33d1fcf57b0f2c3d77bf4a96.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fa/e4ada1a57cc57f33d1fcf57b0f2c3d77bf4a96.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/4ded38c8534e301ce0ad9ebadfeba22d121aa7.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/4ded38c8534e301ce0ad9ebadfeba22d121aa7.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/4ded38c8534e301ce0ad9ebadfeba22d121aa7.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b0
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b0/9ff55811c422618c93e959d9760f207574ae6c.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b0/9ff55811c422618c93e959d9760f207574ae6c.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/b0/9ff55811c422618c93e959d9760f207574ae6c.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9f/248496dc964c2905d37a52a320215097e8c5e4.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9f/248496dc964c2905d37a52a320215097e8c5e4.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9f/248496dc964c2905d37a52a320215097e8c5e4.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam 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)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=61a9dfbfe3cde373f3a3b42c89a28190907e3cfd 714835c46354336bbcf9e71ddf24eeed56ab6a3d 884ded38c8534e301ce0ad9ebadfeba22d [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1570,16 +1669,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_i386.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_i386.deb'.
- dpkg-genchanges -B -mamd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org> >../samtools_1.2-3_i386.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_i386.deb'.
+ dpkg-genchanges -B -mamd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org> >../samtools_1.2-4_i386.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1608
+Build finished at 20151221-1319
Finished
────────
@@ -1596,54 +1701,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_i386.changes:
+samtools_1.2-4_i386.changes:
────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: i386
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
Maintainer: amd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- 97c12ab7015984dfe7c3e0faf2a039c00b9e2cde 407944 samtools_1.2-3_i386.deb
+ b9e0db8ff6f869b5a76124828c98f6cafe12873d 383882 samtools-dbgsym_1.2-4_i386.deb
+ 97389cb22465c9f9bacb6353c4733caefe4bf43e 408656 samtools_1.2-4_i386.deb
Checksums-Sha256:
- e8d7b5d48c3dd064e6a12ba055e456aa4d518920e9262fc38cee065f3c56f221 407944 samtools_1.2-3_i386.deb
+ dee644872fb7f6f12330686e17492f8e7648a0891900228c20c5e030008ebaef 383882 samtools-dbgsym_1.2-4_i386.deb
+ 6ebb72cf1f431bc269a84dc63ce7734bfcfbe6ca56984c2f6976ecb5cef8863b 408656 samtools_1.2-4_i386.deb
Files:
- c2b8bbf29c4c95809d739ba42bc3839d 407944 science optional samtools_1.2-3_i386.deb
+ c2f9e4e188f35d3b5216d0dd3687e57b 383882 debug extra samtools-dbgsym_1.2-4_i386.deb
+ 9c55bf0a21fd7966757c30b57db5b147 408656 science optional samtools_1.2-4_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_i386.deb
+samtools-dbgsym_1.2-4_i386.deb
+──────────────────────────────
+
+ new debian package, version 2.0.
+ size 383882 bytes: control archive=813 bytes.
+ 645 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: i386
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 450
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 61a9dfbfe3cde373f3a3b42c89a28190907e3cfd 714835c46354336bbcf9e71ddf24eeed56ab6a3d 884ded38c8534e301ce0ad9ebadfeba22d121aa7 9f248496dc964c2905d37a52a320215097e8c5e4 b09ff55811c422618c93e959d9760f207574ae6c b9edc7147ae8f6f460e1369e71c4c7dfca62ec9d fae4ada1a57cc57f33d1fcf57b0f2c3d77bf4a96
+
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/61/
+-rw-r--r-- root/root 11760 2015-12-21 13:19 ./usr/lib/debug/.build-id/61/a9dfbfe3cde373f3a3b42c89a28190907e3cfd.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/71/
+-rw-r--r-- root/root 9176 2015-12-21 13:19 ./usr/lib/debug/.build-id/71/4835c46354336bbcf9e71ddf24eeed56ab6a3d.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/88/
+-rw-r--r-- root/root 9468 2015-12-21 13:19 ./usr/lib/debug/.build-id/88/4ded38c8534e301ce0ad9ebadfeba22d121aa7.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/9f/
+-rw-r--r-- root/root 367020 2015-12-21 13:19 ./usr/lib/debug/.build-id/9f/248496dc964c2905d37a52a320215097e8c5e4.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/b0/
+-rw-r--r-- root/root 18184 2015-12-21 13:19 ./usr/lib/debug/.build-id/b0/9ff55811c422618c93e959d9760f207574ae6c.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/b9/
+-rw-r--r-- root/root 16248 2015-12-21 13:19 ./usr/lib/debug/.build-id/b9/edc7147ae8f6f460e1369e71c4c7dfca62ec9d.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/fa/
+-rw-r--r-- root/root 9468 2015-12-21 13:19 ./usr/lib/debug/.build-id/fa/e4ada1a57cc57f33d1fcf57b0f2c3d77bf4a96.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 13:19 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_i386.deb
───────────────────────
new debian package, version 2.0.
- size 407944 bytes: control archive=1483 bytes.
- 802 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 408656 bytes: control archive=1604 bytes.
+ 807 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1111
+ Installed-Size: 1113
Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1653,44 +1811,51 @@ samtools_1.2-3_i386.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 16:08 ./
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/bin/
--rwxr-xr-x root/root 17812 2015-09-22 16:08 ./usr/bin/ace2sam
+ one 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 2015-12-21 13:19 ./
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/bin/
+-rwxr-xr-x root/root 17956 2015-12-21 13:19 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 9600 2015-09-22 16:08 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 9600 2015-09-22 16:08 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 13696 2015-09-22 16:08 ./usr/bin/md5fa
--rwxr-xr-x root/root 9572 2015-09-22 16:08 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 9748 2015-12-21 13:19 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2015-12-21 13:19 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13840 2015-12-21 13:19 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9716 2015-12-21 13:19 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 866564 2015-09-22 16:08 ./usr/bin/samtools
+-rwxr-xr-x root/root 862616 2015-12-21 13:19 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 17872 2015-09-22 16:08 ./usr/bin/wgsim
+-rwxr-xr-x root/root 18020 2015-12-21 13:19 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 16:08 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 13:19 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 13:19 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 13:19 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 13:19 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1710,23 +1875,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: i386
-Build-Space: 15080
-Build-Time: 83
+Build-Space: 15936
+Build-Time: 86
Distribution: sid
Host Architecture: i386
-Install-Time: 11
-Job: samtools_1.2-3
+Install-Time: 13
+Job: samtools_1.2-4
Machine Architecture: amd64
Package: samtools
-Package-Time: 117
-Source-Version: 1.2-3
-Space: 15080
+Package-Time: 118
+Source-Version: 1.2-4
+Space: 15936
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1608
-Build needed 00:01:57, 15080k disc space
-Signature with key 'F5E1965F' requested:
- signfile /home/buildd/build/samtools_1.2-3_i386.changes F5E1965F
+Finished at 20151221-1319
+Build needed 00:01:58, 15936k disc space
+Signature with key '88464D8B' requested:
+ signfile /home/buildd/build/samtools_1.2-4_i386.changes 88464D8B
Successfully signed changes file
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index f16fdcf..b9a9472 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,46 +1,47 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fano.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fayrfax.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (kfreebsd-amd64) 22 Sep 2015 17:23 ║
+║ samtools 1.2-4 (kfreebsd-amd64) 21 Dec 2015 13:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: kfreebsd-amd64
Host Architecture: kfreebsd-amd64
Build Architecture: kfreebsd-amd64
-I: NOTICE: Log filtering will replace 'build/samtools-qWsSJB/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-qWsSJB' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-kfreebsd-amd64-sbuild-1442942612-57690' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-aMMNEA/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-aMMNEA' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-a-sbuild-1450703851-16756' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror-ubc.debian.org unstable InRelease [253 kB]
-Get:2 http://mirror-ubc.debian.org unstable/main Sources [8093 kB]
-Get:3 http://ftp.debian.org unstable InRelease [253 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [59.7 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [106 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [6980 kB]
-Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [42.6 kB]
-Get:9 http://incoming.debian.org buildd-unstable/main Sources [356 kB]
-Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1252 B]
-Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [84.0 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [1064 B]
-Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:17 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [6980 kB]
-Get:18 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [42.6 kB]
-Fetched 31.6 MB in 13s (2356 kB/s)
+Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:2 http://ftp.de.debian.org/debian unstable InRelease [265 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [203 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-amd64 Packages [137 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-amd64 Packages [568 B]
+Get:10 http://ftp.de.debian.org/debian unstable/main Sources [8421 kB]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-amd64 Packages [7341 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [45.1 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [105 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 Packages [7341 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [45.1 kB]
+Fetched 32.9 MB in 4s (6788 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 4s (1022 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 0s (7618 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-ytP0Ls/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-d0e_ot/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]
+Get:1 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ Packages [530 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/776 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-d0e_ot/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
+debconf: delaying package configuration, since apt-utils is not installed
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 ... 11308 files and directories currently installed.)
+(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 ... 12027 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, 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, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, 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-qlG7Zs/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-9ii9Cr/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]
+Get:1 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Sources [472 B]
+Get:5 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ Packages [736 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 18.0 MB/18.0 MB of archives.
-After this operation, 64.4 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.3-1 [1077 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.6 [183 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.4.1-1 [28.0 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.3-1 [997 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.2.1-3 [19.4 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.1-1 [2397 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libicu55 kfreebsd-amd64 55.1-5 [7649 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.2+zdfsg1-4 [888 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3+b1 [135 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2+b1 [287 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.25-1 [255 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.25-1 [61.6 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.6-1 [122 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.6-1 [1457 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-amd64 1.2.1-1 [229 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-amd64 1.2.1-1 [277 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main libio-pty-perl kfreebsd-amd64 1:1.08-1+b4 [36.0 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 6.0+20150810-1 [77.6 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 6.0+20150810-1 [171 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-amd64 1.2.1-1 [223 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2+b1 [206 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
+Need to get 18.2 MB/18.2 MB of archives.
+After this operation, 65.1 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-9ii9Cr/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [980 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 groff-base kfreebsd-amd64 1.22.3-4 [1077 kB]
+Get:4 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 bsdmainutils kfreebsd-amd64 9.0.6+b1 [183 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libpipeline1 kfreebsd-amd64 1.4.1-1 [28.0 kB]
+Get:6 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 man-db kfreebsd-amd64 2.7.5-1 [999 kB]
+Get:7 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libffi6 kfreebsd-amd64 3.2.1-4 [19.8 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libglib2.0-0 kfreebsd-amd64 2.42.1-1 [2397 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libunistring0 kfreebsd-amd64 0.9.3-5.2+b1 [287 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libmagic1 kfreebsd-amd64 1:5.25-2 [255 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 file kfreebsd-amd64 1:5.25-2 [61.6 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 gettext-base kfreebsd-amd64 0.19.6-1 [122 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libicu55 kfreebsd-amd64 55.1-6 [7651 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libxml2 kfreebsd-amd64 2.9.3+dfsg1-1 [888 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libcroco3 kfreebsd-amd64 0.6.11-1 [143 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 gettext kfreebsd-amd64 0.19.6-1 [1457 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 po-debconf all 1.0.18 [248 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 debhelper all 9.20151220 [830 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts1 kfreebsd-amd64 1.2.1-2 [228 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts-dev kfreebsd-amd64 1.2.1-2 [278 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libio-pty-perl kfreebsd-amd64 1:1.08-1.1+b1 [33.7 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtinfo-dev kfreebsd-amd64 6.0+20151024-2 [77.4 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libncurses5-dev kfreebsd-amd64 6.0+20151024-2 [174 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 tabix kfreebsd-amd64 1.2.1-2 [223 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2+b1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.0 MB in 1s (14.6 MB/s)
+Fetched 18.2 MB in 2s (6898 kB/s)
Selecting previously unselected package bash-completion.
-(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 ... 11308 files and directories currently installed.)
+(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 ... 12027 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_kfreebsd-amd64.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_kfreebsd-amd64.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_kfreebsd-amd64.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_kfreebsd-amd64.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
Preparing to unpack .../libpipeline1_1.4.1-1_kfreebsd-amd64.deb ...
Unpacking libpipeline1:kfreebsd-amd64 (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_kfreebsd-amd64.deb ...
-Unpacking man-db (2.7.3-1) ...
+Preparing to unpack .../man-db_2.7.5-1_kfreebsd-amd64.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libffi6:kfreebsd-amd64.
-Preparing to unpack .../libffi6_3.2.1-3_kfreebsd-amd64.deb ...
-Unpacking libffi6:kfreebsd-amd64 (3.2.1-3) ...
+Preparing to unpack .../libffi6_3.2.1-4_kfreebsd-amd64.deb ...
+Unpacking libffi6:kfreebsd-amd64 (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
Preparing to unpack .../libglib2.0-0_2.42.1-1_kfreebsd-amd64.deb ...
Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ...
-Selecting previously unselected package libicu55:kfreebsd-amd64.
-Preparing to unpack .../libicu55_55.1-5_kfreebsd-amd64.deb ...
-Unpacking libicu55:kfreebsd-amd64 (55.1-5) ...
-Selecting previously unselected package libxml2:kfreebsd-amd64.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_kfreebsd-amd64.deb ...
-Unpacking libxml2:kfreebsd-amd64 (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:kfreebsd-amd64.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_kfreebsd-amd64.deb ...
-Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ...
Selecting previously unselected package libunistring0:kfreebsd-amd64.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_kfreebsd-amd64.deb ...
Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:kfreebsd-amd64.
-Preparing to unpack .../libmagic1_1%3a5.25-1_kfreebsd-amd64.deb ...
-Unpacking libmagic1:kfreebsd-amd64 (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_kfreebsd-amd64.deb ...
+Unpacking libmagic1:kfreebsd-amd64 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_kfreebsd-amd64.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_kfreebsd-amd64.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_kfreebsd-amd64.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:kfreebsd-amd64.
+Preparing to unpack .../libicu55_55.1-6_kfreebsd-amd64.deb ...
+Unpacking libicu55:kfreebsd-amd64 (55.1-6) ...
+Selecting previously unselected package libxml2:kfreebsd-amd64.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_kfreebsd-amd64.deb ...
+Unpacking libxml2:kfreebsd-amd64 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libcroco3:kfreebsd-amd64.
+Preparing to unpack .../libcroco3_0.6.11-1_kfreebsd-amd64.deb ...
+Unpacking libcroco3:kfreebsd-amd64 (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_kfreebsd-amd64.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:kfreebsd-amd64.
-Preparing to unpack .../libhts1_1.2.1-1_kfreebsd-amd64.deb ...
-Unpacking libhts1:kfreebsd-amd64 (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_kfreebsd-amd64.deb ...
+Unpacking libhts1:kfreebsd-amd64 (1.2.1-2) ...
Selecting previously unselected package libhts-dev:kfreebsd-amd64.
-Preparing to unpack .../libhts-dev_1.2.1-1_kfreebsd-amd64.deb ...
-Unpacking libhts-dev:kfreebsd-amd64 (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_kfreebsd-amd64.deb ...
+Unpacking libhts-dev:kfreebsd-amd64 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_kfreebsd-amd64.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_kfreebsd-amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_kfreebsd-amd64.deb ...
-Unpacking libtinfo-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_kfreebsd-amd64.deb ...
+Unpacking libtinfo-dev:kfreebsd-amd64 (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_kfreebsd-amd64.deb ...
-Unpacking libncurses5-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_kfreebsd-amd64.deb ...
+Unpacking libncurses5-dev:kfreebsd-amd64 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_kfreebsd-amd64.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_kfreebsd-amd64.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_kfreebsd-amd64.deb ...
Unpacking zlib1g-dev:kfreebsd-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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:kfreebsd-amd64 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:kfreebsd-amd64 (3.2.1-3) ...
+Setting up libffi6:kfreebsd-amd64 (3.2.1-4) ...
Setting up libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ...
No schema files found: doing nothing.
-Setting up libicu55:kfreebsd-amd64 (55.1-5) ...
-Setting up libxml2:kfreebsd-amd64 (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ...
Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
-Setting up libmagic1:kfreebsd-amd64 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:kfreebsd-amd64 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:kfreebsd-amd64 (55.1-6) ...
+Setting up libxml2:kfreebsd-amd64 (2.9.3+dfsg1-1) ...
+Setting up libcroco3:kfreebsd-amd64 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:kfreebsd-amd64 (1.2.1-1) ...
-Setting up libhts-dev:kfreebsd-amd64 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:kfreebsd-amd64 (6.0+20150810-1) ...
-Setting up libncurses5-dev:kfreebsd-amd64 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:kfreebsd-amd64 (1.2.1-2) ...
+Setting up libhts-dev:kfreebsd-amd64 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:kfreebsd-amd64 (6.0+20151024-2) ...
+Setting up libncurses5-dev:kfreebsd-amd64 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: GNU/kFreeBSD 10.1-0-amd64 kfreebsd-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 kfreebsd-kernel-headers_10.1~5 libc0.1-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17
-Package versions: 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_1:2.27-3 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 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-1 findutils_4.4 [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2f [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -322,11 +367,11 @@ HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-kfreebsd-amd64-sbuild
-SCHROOT_CHROOT_NAME=sid-kfreebsd-amd64-sbuild
+SCHROOT_CHROOT_NAME=sid-k-a-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-kfreebsd-amd64-sbuild-1442942612-57690
+SCHROOT_SESSION_ID=sid-k-a-sbuild-1450703851-16756
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -337,7 +382,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture kfreebsd-amd64
@@ -475,82 +520,82 @@ dh_auto_test -- \
make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-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/hbsGdk3of9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/aHQAAjFh4l/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/hbsGdk3of9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/aHQAAjFh4l/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/hbsGdk3of9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/aHQAAjFh4l/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/hbsGdk3of9/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/aHQAAjFh4l/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/hbsGdk3of9/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/aHQAAjFh4l/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/hbsGdk3of9/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/aHQAAjFh4l/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/hbsGdk3of9/mpileup.bam.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/aHQAAjFh4l/mpileup.bam.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/hbsGdk3of9/mpileup.bam.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/aHQAAjFh4l/mpileup.bam.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/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/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/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/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/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/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/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/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hbsGdk3of9/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/aHQAAjFh4l/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hbsGdk3of9/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:1050-1060 /tmp/aHQAAjFh4l/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -780,80 +825,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/hbsGdk3of9/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/hbsGdk3of9/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/hbsGdk3of9/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/hbsGdk3of9/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.test067.sam -h -l Library 2 /tmp/hbsGdk3of9/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/aHQAAjFh4l/view.test067.sam -h -l Library 2 /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.test069.sam -h -l Library 2 /tmp/hbsGdk3of9/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/aHQAAjFh4l/view.test069.sam -h -l Library 2 /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.test071.sam -h -l Library 2 /tmp/hbsGdk3of9/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/aHQAAjFh4l/view.test071.sam -h -l Library 2 /tmp/aHQAAjFh4l/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/hbsGdk3of9/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/aHQAAjFh4l/view.test006.cram
.. expected failure
@@ -1300,82 +1345,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/hbsGdk3of9/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/aHQAAjFh4l/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/hbsGdk3of9/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/aHQAAjFh4l/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/hbsGdk3of9/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/aHQAAjFh4l/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/hbsGdk3of9/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/aHQAAjFh4l/depad.001p.bam
.. expected failure
@@ -1413,7 +1458,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/VlizHCAsyu - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/QNepMGrILs - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1507,6 +1552,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1522,14 +1570,27 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1537,31 +1598,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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-kfreebsd-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/lib/x86_64-kfreebsd-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c7
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c7/8eb0a6c2084112f97607b38caf4e91f8b16314.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c7/8eb0a6c2084112f97607b38caf4e91f8b16314.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c7/8eb0a6c2084112f97607b38caf4e91f8b16314.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/49
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/49/610c763c1ed05f0276c322906af8a7c033d3e7.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/49/610c763c1ed05f0276c322906af8a7c033d3e7.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/49/610c763c1ed05f0276c322906af8a7c033d3e7.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5e/d6d38f52e5391edba797247303439fa2aa4502.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5e/d6d38f52e5391edba797247303439fa2aa4502.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5e/d6d38f52e5391edba797247303439fa2aa4502.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/092509e86dc5a1f8afe57302a786d7854c4746.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/092509e86dc5a1f8afe57302a786d7854c4746.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/092509e86dc5a1f8afe57302a786d7854c4746.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c0
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c0/7b9128ec4a6278d9fe598949fd1ddd87a8ae72.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c0/7b9128ec4a6278d9fe598949fd1ddd87a8ae72.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c0/7b9128ec4a6278d9fe598949fd1ddd87a8ae72.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5b
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5b/8ad4665f32c41f69358afacf148c3969b320df.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5b/8ad4665f32c41f69358afacf148c3969b320df.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5b/8ad4665f32c41f69358afacf148c3969b320df.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/33
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/33/77da7d4ae122900a170a9f337d22bd5406ed3f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/33/77da7d4ae122900a170a9f337d22bd5406ed3f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/33/77da7d4ae122900a170a9f337d22bd5406ed3f.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short 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)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=28092509e86dc5a1f8afe57302a786d7854c4746 3377da7d4ae122900a170a9f337d22bd5406ed3f 49610c763c1ed05f0276c322906af8a7c0 [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1571,16 +1668,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_kfreebsd-amd64.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_1.2-3_kfreebsd-amd64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org> >../samtools_1.2-4_kfreebsd-amd64.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1726
+Build finished at 20151221-1319
Finished
────────
@@ -1597,54 +1700,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_kfreebsd-amd64.changes:
+samtools_1.2-4_kfreebsd-amd64.changes:
──────────────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-amd64
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Maintainer: kfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- e712b8291a20a1fcfcb86c7275b8a507e2b465ee 394868 samtools_1.2-3_kfreebsd-amd64.deb
+ 906cb5118c87f18d8352bafb88f27e3587dea807 416274 samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
+ 302eca107188c6e20432af89d93d5f845c3df4ff 395900 samtools_1.2-4_kfreebsd-amd64.deb
Checksums-Sha256:
- c7b3870dbcf43ce2f0b1de042a1f2bf0bb8afd5713d87ccd594b40111a4b62ed 394868 samtools_1.2-3_kfreebsd-amd64.deb
+ bdaebd1039c93e96bc70ca2a5a30748c23d8172bcaa76d15ba478219b7c7fb54 416274 samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
+ 299fc1830ee4795be104f1d57fcee93a1daf2a79aac488461dd7472cc23e4f96 395900 samtools_1.2-4_kfreebsd-amd64.deb
Files:
- a4b1bfd85a27ca939e50f4f1d2871499 394868 science optional samtools_1.2-3_kfreebsd-amd64.deb
+ 1df8aadd1de5b703d97983aae5f702fe 416274 debug extra samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
+ 544eccdf94e78f7cac3e399617e09950 395900 science optional samtools_1.2-4_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_kfreebsd-amd64.deb
+samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
+────────────────────────────────────────
+
+ new debian package, version 2.0.
+ size 416274 bytes: control archive=821 bytes.
+ 655 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: kfreebsd-amd64
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 506
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 28092509e86dc5a1f8afe57302a786d7854c4746 3377da7d4ae122900a170a9f337d22bd5406ed3f 49610c763c1ed05f0276c322906af8a7c033d3e7 5b8ad4665f32c41f69358afacf148c3969b320df 5ed6d38f52e5391edba797247303439fa2aa4502 c07b9128ec4a6278d9fe598949fd1ddd87a8ae72 c78eb0a6c2084112f97607b38caf4e91f8b16314
+
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/28/
+-rw-r--r-- root/root 11816 2015-12-21 13:19 ./usr/lib/debug/.build-id/28/092509e86dc5a1f8afe57302a786d7854c4746.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/33/
+-rw-r--r-- root/root 19056 2015-12-21 13:19 ./usr/lib/debug/.build-id/33/77da7d4ae122900a170a9f337d22bd5406ed3f.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/49/
+-rw-r--r-- root/root 20776 2015-12-21 13:19 ./usr/lib/debug/.build-id/49/610c763c1ed05f0276c322906af8a7c033d3e7.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/5b/
+-rw-r--r-- root/root 11544 2015-12-21 13:19 ./usr/lib/debug/.build-id/5b/8ad4665f32c41f69358afacf148c3969b320df.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/5e/
+-rw-r--r-- root/root 11824 2015-12-21 13:19 ./usr/lib/debug/.build-id/5e/d6d38f52e5391edba797247303439fa2aa4502.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/c0/
+-rw-r--r-- root/root 14456 2015-12-21 13:19 ./usr/lib/debug/.build-id/c0/7b9128ec4a6278d9fe598949fd1ddd87a8ae72.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/lib/debug/.build-id/c7/
+-rw-r--r-- root/root 408040 2015-12-21 13:19 ./usr/lib/debug/.build-id/c7/8eb0a6c2084112f97607b38caf4e91f8b16314.debug
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_kfreebsd-amd64.deb
─────────────────────────────────
new debian package, version 2.0.
- size 394868 bytes: control archive=1496 bytes.
- 817 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 395900 bytes: control archive=1616 bytes.
+ 822 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1070
+ Installed-Size: 1068
Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1654,44 +1810,51 @@ samtools_1.2-3_kfreebsd-amd64.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 17:26 ./
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/bin/
--rwxr-xr-x root/root 22664 2015-09-22 17:26 ./usr/bin/ace2sam
+ one 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 2015-12-21 13:19 ./
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/bin/
+-rwxr-xr-x root/root 22856 2015-12-21 13:19 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 10336 2015-09-22 17:26 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10336 2015-09-22 17:26 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14440 2015-09-22 17:26 ./usr/bin/md5fa
--rwxr-xr-x root/root 10280 2015-09-22 17:26 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 10536 2015-12-21 13:19 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10536 2015-12-21 13:19 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14632 2015-12-21 13:19 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10472 2015-12-21 13:19 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 810616 2015-09-22 17:26 ./usr/bin/samtools
+-rwxr-xr-x root/root 802624 2015-12-21 13:19 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 22752 2015-09-22 17:26 ./usr/bin/wgsim
+-rwxr-xr-x root/root 22944 2015-12-21 13:19 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 17:26 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 13:19 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 13:19 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 13:19 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 13:19 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 13:19 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1711,23 +1874,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-amd64
-Build-Space: 15836
-Build-Time: 103
+Build-Space: 16920
+Build-Time: 87
Distribution: sid
Host Architecture: kfreebsd-amd64
-Install-Time: 20
-Job: samtools_1.2-3
+Install-Time: 15
+Job: samtools_1.2-4
Machine Architecture: kfreebsd-amd64
Package: samtools
-Package-Time: 178
-Source-Version: 1.2-3
-Space: 15836
+Package-Time: 128
+Source-Version: 1.2-4
+Space: 16920
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1726
-Build needed 00:02:58, 15836k disc space
-Signature with key '33251A36' requested:
- signfile /home/buildd/build/samtools_1.2-3_kfreebsd-amd64.changes 33251A36
+Finished at 20151221-1319
+Build needed 00:02:08, 16920k disc space
+Signature with key '214E2A08' requested:
+ signfile /home/buildd/build/samtools_1.2-4_kfreebsd-amd64.changes 214E2A08
Successfully signed changes file
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 67f4b71..f0bd803 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -2,45 +2,46 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fils.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (kfreebsd-i386) 22 Sep 2015 18:09 ║
+║ samtools 1.2-4 (kfreebsd-i386) 21 Dec 2015 13:20 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: kfreebsd-i386
Host Architecture: kfreebsd-i386
Build Architecture: kfreebsd-i386
-I: NOTICE: Log filtering will replace 'build/samtools-ZiSBO4/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-ZiSBO4' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-kfreebsd-i386-sbuild-1442945363-90721' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-q3QEe1/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-q3QEe1' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-i-sbuild-1450704051-17953' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.de.debian.org unstable InRelease [253 kB]
-Get:2 http://ftp.debian.org unstable InRelease [253 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:4 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:5 http://ftp.de.debian.org unstable/main Sources [8093 kB]
-Get:6 http://incoming.debian.org buildd-unstable/main Sources [361 kB]
-Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1252 B]
-Get:9 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [111 kB]
-Get:10 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [1064 B]
-Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:13 http://ftp.debian.org unstable/main kfreebsd-i386 Packages [6969 kB]
-Get:14 http://ftp.de.debian.org unstable/contrib Sources [59.7 kB]
-Get:15 http://ftp.de.debian.org unstable/non-free Sources [106 kB]
-Get:16 http://ftp.de.debian.org unstable/main kfreebsd-i386 Packages [6969 kB]
-Get:17 http://ftp.debian.org unstable/contrib kfreebsd-i386 Packages [42.6 kB]
-Get:18 http://ftp.de.debian.org unstable/contrib kfreebsd-i386 Packages [42.6 kB]
-Fetched 31.6 MB in 16s (1913 kB/s)
+Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 http://ftp.de.debian.org/debian unstable InRelease [265 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [203 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-i386 Packages [135 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-i386 Packages [568 B]
+Get:9 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/main Sources [8421 kB]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-i386 Packages [7331 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-i386 Packages [45.0 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [105 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 Packages [7331 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-i386 Packages [45.0 kB]
+Fetched 32.9 MB in 6s (5285 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 1s (2697 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 0s (7632 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-eiSkMa/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-663JgF/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]
+Get:1 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ Packages [533 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B/776 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-663JgF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
+debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
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(Reading database ... 10952 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 11668 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, 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, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, 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-Oz6xSm/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-dtQOBh/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]
+Get:1 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Sources [472 B]
+Get:5 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ Packages [734 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 18.3 MB/18.3 MB of archives.
-After this operation, 64.6 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.3-1 [1099 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.6 [183 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.4.1-1 [29.8 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.7.3-1 [1006 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi6 kfreebsd-i386 3.2.1-3 [18.4 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.42.1-1 [2455 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libicu55 kfreebsd-i386 55.1-5 [7761 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.9.2+zdfsg1-4 [920 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.8-3+b1 [141 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5.2+b1 [285 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.25-1 [261 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.25-1 [61.5 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.19.6-1 [123 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.19.6-1 [1461 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libhts1 kfreebsd-i386 1.2.1-1 [241 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main libhts-dev kfreebsd-i386 1.2.1-1 [283 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main libio-pty-perl kfreebsd-i386 1:1.08-1+b4 [36.5 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 6.0+20150810-1 [76.4 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 6.0+20150810-1 [173 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main tabix kfreebsd-i386 1.2.1-1 [231 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-2+b1 [205 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
+Need to get 18.5 MB/18.5 MB of archives.
+After this operation, 65.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-dtQOBh/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [980 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 groff-base kfreebsd-i386 1.22.3-4 [1100 kB]
+Get:4 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 bsdmainutils kfreebsd-i386 9.0.6+b1 [183 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libpipeline1 kfreebsd-i386 1.4.1-1 [29.8 kB]
+Get:6 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 man-db kfreebsd-i386 2.7.5-1 [1007 kB]
+Get:7 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libffi6 kfreebsd-i386 3.2.1-4 [18.8 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libglib2.0-0 kfreebsd-i386 2.42.1-1 [2455 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libunistring0 kfreebsd-i386 0.9.3-5.2+b1 [285 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libmagic1 kfreebsd-i386 1:5.25-2 [261 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 file kfreebsd-i386 1:5.25-2 [61.5 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext-base kfreebsd-i386 0.19.6-1 [123 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libicu55 kfreebsd-i386 55.1-6 [7763 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libxml2 kfreebsd-i386 2.9.3+dfsg1-1 [923 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcroco3 kfreebsd-i386 0.6.11-1 [149 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext kfreebsd-i386 0.19.6-1 [1461 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 po-debconf all 1.0.18 [248 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 debhelper all 9.20151220 [830 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts1 kfreebsd-i386 1.2.1-2 [245 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts-dev kfreebsd-i386 1.2.1-2 [283 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libio-pty-perl kfreebsd-i386 1:1.08-1.1+b1 [34.2 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtinfo-dev kfreebsd-i386 6.0+20151024-2 [76.3 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libncurses5-dev kfreebsd-i386 6.0+20151024-2 [176 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 tabix kfreebsd-i386 1.2.1-2 [231 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.3 MB in 2s (8043 kB/s)
+Fetched 18.5 MB in 1s (12.3 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 25%
(Reading database ... 30%
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(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 ... 10952 files and directories currently installed.)
+(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%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11668 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_kfreebsd-i386.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_kfreebsd-i386.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_kfreebsd-i386.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_kfreebsd-i386.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:kfreebsd-i386.
Preparing to unpack .../libpipeline1_1.4.1-1_kfreebsd-i386.deb ...
Unpacking libpipeline1:kfreebsd-i386 (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_kfreebsd-i386.deb ...
-Unpacking man-db (2.7.3-1) ...
+Preparing to unpack .../man-db_2.7.5-1_kfreebsd-i386.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libffi6:kfreebsd-i386.
-Preparing to unpack .../libffi6_3.2.1-3_kfreebsd-i386.deb ...
-Unpacking libffi6:kfreebsd-i386 (3.2.1-3) ...
+Preparing to unpack .../libffi6_3.2.1-4_kfreebsd-i386.deb ...
+Unpacking libffi6:kfreebsd-i386 (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
Preparing to unpack .../libglib2.0-0_2.42.1-1_kfreebsd-i386.deb ...
Unpacking libglib2.0-0:kfreebsd-i386 (2.42.1-1) ...
-Selecting previously unselected package libicu55:kfreebsd-i386.
-Preparing to unpack .../libicu55_55.1-5_kfreebsd-i386.deb ...
-Unpacking libicu55:kfreebsd-i386 (55.1-5) ...
-Selecting previously unselected package libxml2:kfreebsd-i386.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_kfreebsd-i386.deb ...
-Unpacking libxml2:kfreebsd-i386 (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:kfreebsd-i386.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_kfreebsd-i386.deb ...
-Unpacking libcroco3:kfreebsd-i386 (0.6.8-3+b1) ...
Selecting previously unselected package libunistring0:kfreebsd-i386.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_kfreebsd-i386.deb ...
Unpacking libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:kfreebsd-i386.
-Preparing to unpack .../libmagic1_1%3a5.25-1_kfreebsd-i386.deb ...
-Unpacking libmagic1:kfreebsd-i386 (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_kfreebsd-i386.deb ...
+Unpacking libmagic1:kfreebsd-i386 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_kfreebsd-i386.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_kfreebsd-i386.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_kfreebsd-i386.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:kfreebsd-i386.
+Preparing to unpack .../libicu55_55.1-6_kfreebsd-i386.deb ...
+Unpacking libicu55:kfreebsd-i386 (55.1-6) ...
+Selecting previously unselected package libxml2:kfreebsd-i386.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_kfreebsd-i386.deb ...
+Unpacking libxml2:kfreebsd-i386 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libcroco3:kfreebsd-i386.
+Preparing to unpack .../libcroco3_0.6.11-1_kfreebsd-i386.deb ...
+Unpacking libcroco3:kfreebsd-i386 (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_kfreebsd-i386.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:kfreebsd-i386.
-Preparing to unpack .../libhts1_1.2.1-1_kfreebsd-i386.deb ...
-Unpacking libhts1:kfreebsd-i386 (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_kfreebsd-i386.deb ...
+Unpacking libhts1:kfreebsd-i386 (1.2.1-2) ...
Selecting previously unselected package libhts-dev:kfreebsd-i386.
-Preparing to unpack .../libhts-dev_1.2.1-1_kfreebsd-i386.deb ...
-Unpacking libhts-dev:kfreebsd-i386 (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_kfreebsd-i386.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_kfreebsd-i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_kfreebsd-i386.deb ...
-Unpacking libtinfo-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_kfreebsd-i386.deb ...
+Unpacking libtinfo-dev:kfreebsd-i386 (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:kfreebsd-i386.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_kfreebsd-i386.deb ...
-Unpacking libncurses5-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_kfreebsd-i386.deb ...
+Unpacking libncurses5-dev:kfreebsd-i386 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_kfreebsd-i386.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_kfreebsd-i386.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_kfreebsd-i386.deb ...
Unpacking zlib1g-dev:kfreebsd-i386 (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:kfreebsd-i386 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:kfreebsd-i386 (3.2.1-3) ...
+Setting up libffi6:kfreebsd-i386 (3.2.1-4) ...
Setting up libglib2.0-0:kfreebsd-i386 (2.42.1-1) ...
No schema files found: doing nothing.
-Setting up libicu55:kfreebsd-i386 (55.1-5) ...
-Setting up libxml2:kfreebsd-i386 (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:kfreebsd-i386 (0.6.8-3+b1) ...
Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
-Setting up libmagic1:kfreebsd-i386 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:kfreebsd-i386 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:kfreebsd-i386 (55.1-6) ...
+Setting up libxml2:kfreebsd-i386 (2.9.3+dfsg1-1) ...
+Setting up libcroco3:kfreebsd-i386 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:kfreebsd-i386 (1.2.1-1) ...
-Setting up libhts-dev:kfreebsd-i386 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:kfreebsd-i386 (6.0+20150810-1) ...
-Setting up libncurses5-dev:kfreebsd-i386 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:kfreebsd-i386 (1.2.1-2) ...
+Setting up libhts-dev:kfreebsd-i386 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:kfreebsd-i386 (6.0+20151024-2) ...
+Setting up libncurses5-dev:kfreebsd-i386 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: GNU/kFreeBSD 10.1-0-686 kfreebsd-i386 (i386)
-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 kfreebsd-kernel-headers_10.1~5 libc0.1-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17
-Package versions: 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_1:2.27-3 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 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-1 findutils_4.4 [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2f [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -322,11 +367,11 @@ HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-kfreebsd-i386-sbuild
-SCHROOT_CHROOT_NAME=sid-kfreebsd-i386-sbuild
+SCHROOT_CHROOT_NAME=sid-k-i-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-kfreebsd-i386-sbuild-1442945363-90721
+SCHROOT_SESSION_ID=sid-k-i-sbuild-1450704051-17953
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -336,7 +381,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture kfreebsd-i386
@@ -474,82 +519,82 @@ dh_auto_test -- \
make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-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/ffJ8jRQaFI/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/lAKSxc6s5Q/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/ffJ8jRQaFI/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lAKSxc6s5Q/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/ffJ8jRQaFI/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lAKSxc6s5Q/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/ffJ8jRQaFI/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/lAKSxc6s5Q/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/ffJ8jRQaFI/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/lAKSxc6s5Q/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/ffJ8jRQaFI/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/lAKSxc6s5Q/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/ffJ8jRQaFI/mpileup.bam.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/lAKSxc6s5Q/mpileup.bam.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ffJ8jRQaFI/mpileup.bam.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/lAKSxc6s5Q/mpileup.bam.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/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/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/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/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ffJ8jRQaFI/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lAKSxc6s5Q/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ffJ8jRQaFI/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lAKSxc6s5Q/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +824,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.test067.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/lAKSxc6s5Q/view.test067.sam -h -l Library 2 /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.test069.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/lAKSxc6s5Q/view.test069.sam -h -l Library 2 /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.test071.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/lAKSxc6s5Q/view.test071.sam -h -l Library 2 /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/lAKSxc6s5Q/view.test006.cram
.. expected failure
@@ -1299,82 +1344,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/ffJ8jRQaFI/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/lAKSxc6s5Q/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/ffJ8jRQaFI/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/lAKSxc6s5Q/depad.001p.bam
.. expected failure
@@ -1412,7 +1457,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/0JNqdc92H7 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/OXlcZpyWfC - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1506,6 +1551,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1521,14 +1569,27 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1536,31 +1597,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/i386-kfreebsd-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/lib/i386-kfreebsd-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/9368e737d5b9c2d7e616498b55c9a14a76cf6f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/9368e737d5b9c2d7e616498b55c9a14a76cf6f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7a/9368e737d5b9c2d7e616498b55c9a14a76cf6f.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cc
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cc/8f2e5d2b764dcdcbb5d0536437607bab1e38e8.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cc/8f2e5d2b764dcdcbb5d0536437607bab1e38e8.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cc/8f2e5d2b764dcdcbb5d0536437607bab1e38e8.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ac
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ac/73346e0958e672784271ac6c36826a8d05db93.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ac/73346e0958e672784271ac6c36826a8d05db93.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ac/73346e0958e672784271ac6c36826a8d05db93.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/2f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/2f/2b0e9e8907d97e233b8b95bb21c88a1c31e990.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/2f/2b0e9e8907d97e233b8b95bb21c88a1c31e990.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/2f/2b0e9e8907d97e233b8b95bb21c88a1c31e990.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d7
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d7/ed48c96ad82d7bc7620976595d208e03079f4b.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d7/ed48c96ad82d7bc7620976595d208e03079f4b.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d7/ed48c96ad82d7bc7620976595d208e03079f4b.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3e/c16de4a00793915327d2c7e19e4bee8635cbb9.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3e/c16de4a00793915327d2c7e19e4bee8635cbb9.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3e/c16de4a00793915327d2c7e19e4bee8635cbb9.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/be081bdcbbfb13622ce73f1818122aab7a978f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/be081bdcbbfb13622ce73f1818122aab7a978f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/be081bdcbbfb13622ce73f1818122aab7a978f.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=2f2b0e9e8907d97e233b8b95bb21c88a1c31e990 3ec16de4a00793915327d2c7e19e4bee8635cbb9 7a9368e737d5b9c2d7e616498b55c9a14a [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1570,16 +1667,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_kfreebsd-i386.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.2-3_kfreebsd-i386.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.2-4_kfreebsd-i386.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1812
+Build finished at 20151221-1323
Finished
────────
@@ -1596,54 +1699,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_kfreebsd-i386.changes:
+samtools_1.2-4_kfreebsd-i386.changes:
─────────────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-i386
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- 47eba0a0ca450914e59152b0e9c7adac88237fbe 408396 samtools_1.2-3_kfreebsd-i386.deb
+ 9f6cca37f8c8d1bb67dd2b8ed80f870853058798 384164 samtools-dbgsym_1.2-4_kfreebsd-i386.deb
+ e9fa91a20011a3b12b028387f5fc9865b96aa75b 409052 samtools_1.2-4_kfreebsd-i386.deb
Checksums-Sha256:
- bd3e2c723b73aa8925ee16069eee7bc5f6668405bd4b82991f6478c718525487 408396 samtools_1.2-3_kfreebsd-i386.deb
+ cd3006cb9e4b49c1e0433ad771726b6e4c873083856f6d20ec7281e85f3f7db9 384164 samtools-dbgsym_1.2-4_kfreebsd-i386.deb
+ 2f4f5f5ab5e9d2e92056908c183562a2005774660715004c411802b5ca7045b2 409052 samtools_1.2-4_kfreebsd-i386.deb
Files:
- 7cc5518b37c2b69965bd8222a604140a 408396 science optional samtools_1.2-3_kfreebsd-i386.deb
+ 786527f96d922591fd1154b37b8033f7 384164 debug extra samtools-dbgsym_1.2-4_kfreebsd-i386.deb
+ 393d48e7505a67e81630508c031d90ed 409052 science optional samtools_1.2-4_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_kfreebsd-i386.deb
+samtools-dbgsym_1.2-4_kfreebsd-i386.deb
+───────────────────────────────────────
+
+ new debian package, version 2.0.
+ size 384164 bytes: control archive=824 bytes.
+ 654 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: kfreebsd-i386
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 450
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 2f2b0e9e8907d97e233b8b95bb21c88a1c31e990 3ec16de4a00793915327d2c7e19e4bee8635cbb9 7a9368e737d5b9c2d7e616498b55c9a14a76cf6f 92be081bdcbbfb13622ce73f1818122aab7a978f ac73346e0958e672784271ac6c36826a8d05db93 cc8f2e5d2b764dcdcbb5d0536437607bab1e38e8 d7ed48c96ad82d7bc7620976595d208e03079f4b
+
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/2f/
+-rw-r--r-- root/root 9476 2015-12-21 13:23 ./usr/lib/debug/.build-id/2f/2b0e9e8907d97e233b8b95bb21c88a1c31e990.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/3e/
+-rw-r--r-- root/root 9176 2015-12-21 13:23 ./usr/lib/debug/.build-id/3e/c16de4a00793915327d2c7e19e4bee8635cbb9.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/7a/
+-rw-r--r-- root/root 367088 2015-12-21 13:23 ./usr/lib/debug/.build-id/7a/9368e737d5b9c2d7e616498b55c9a14a76cf6f.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/92/
+-rw-r--r-- root/root 16260 2015-12-21 13:23 ./usr/lib/debug/.build-id/92/be081bdcbbfb13622ce73f1818122aab7a978f.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/ac/
+-rw-r--r-- root/root 9472 2015-12-21 13:23 ./usr/lib/debug/.build-id/ac/73346e0958e672784271ac6c36826a8d05db93.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/cc/
+-rw-r--r-- root/root 18164 2015-12-21 13:23 ./usr/lib/debug/.build-id/cc/8f2e5d2b764dcdcbb5d0536437607bab1e38e8.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/lib/debug/.build-id/d7/
+-rw-r--r-- root/root 11748 2015-12-21 13:23 ./usr/lib/debug/.build-id/d7/ed48c96ad82d7bc7620976595d208e03079f4b.debug
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2015-12-21 13:23 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_kfreebsd-i386.deb
────────────────────────────────
new debian package, version 2.0.
- size 408396 bytes: control archive=1496 bytes.
- 816 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 409052 bytes: control archive=1615 bytes.
+ 821 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1111
+ Installed-Size: 1113
Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1653,44 +1809,51 @@ samtools_1.2-3_kfreebsd-i386.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 18:11 ./
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/bin/
--rwxr-xr-x root/root 17812 2015-09-22 18:11 ./usr/bin/ace2sam
+ one 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 2015-12-21 13:23 ./
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/bin/
+-rwxr-xr-x root/root 17956 2015-12-21 13:23 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 9600 2015-09-22 18:11 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 9600 2015-09-22 18:11 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 13696 2015-09-22 18:11 ./usr/bin/md5fa
--rwxr-xr-x root/root 9572 2015-09-22 18:11 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 9748 2015-12-21 13:23 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2015-12-21 13:23 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13840 2015-12-21 13:23 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9716 2015-12-21 13:23 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 866564 2015-09-22 18:11 ./usr/bin/samtools
+-rwxr-xr-x root/root 862616 2015-12-21 13:23 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 17872 2015-09-22 18:11 ./usr/bin/wgsim
+-rwxr-xr-x root/root 18020 2015-12-21 13:23 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 18:11 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 13:23 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 13:23 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 13:23 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 13:23 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 13:23 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1710,23 +1873,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-i386
-Build-Space: 15540
+Build-Space: 16532
Build-Time: 103
Distribution: sid
Host Architecture: kfreebsd-i386
-Install-Time: 16
-Job: samtools_1.2-3
+Install-Time: 17
+Job: samtools_1.2-4
Machine Architecture: kfreebsd-i386
Package: samtools
-Package-Time: 160
-Source-Version: 1.2-3
-Space: 15540
+Package-Time: 150
+Source-Version: 1.2-4
+Space: 16532
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1812
-Build needed 00:02:40, 15540k disc space
+Finished at 20151221-1323
+Build needed 00:02:30, 16532k disc space
Signature with key 'E3D16566' requested:
- signfile /home/buildd/build/samtools_1.2-3_kfreebsd-i386.changes E3D16566
+ signfile /home/buildd/build/samtools_1.2-4_kfreebsd-i386.changes E3D16566
Successfully signed changes file
diff --git a/m68k.log b/m68k.log
new file mode 100644
index 0000000..ce28d6c
--- /dev/null
+++ b/m68k.log
@@ -0,0 +1,106 @@
+
+sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on wario.physik.fu-berlin.de
+
++==============================================================================+
+| samtools 1.2-4 (m68k) 19 Jan 2016 21:30 |
++==============================================================================+
+
+Package: samtools
+Version: 1.2-4
+Source Version: 1.2-4
+Distribution: sid
+Machine Architecture: m68k
+Host Architecture: m68k
+Build Architecture: m68k
+
+I: NOTICE: Log filtering will replace 'build/samtools-ws26HQ/samtools-1.2' with '<<PKGBUILDDIR>>'
+I: NOTICE: Log filtering will replace 'build/samtools-ws26HQ' with '<<BUILDDIR>>'
+I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-m68k-sbuild-347413bb-fa2f-45ff-becd-4244be3a01a7' with '<<CHROOT>>'
+
++------------------------------------------------------------------------------+
+| Update chroot |
++------------------------------------------------------------------------------+
+
+Hit http://ftp.debian.org unstable InRelease
+Get:1 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:2 http://ftp.debian-ports.org unstable InRelease [37.1 kB]
+Ign http://incoming.debian-ports.org unstable InRelease
+Get:3 http://incoming.debian-ports.org unstable Release.gpg [836 B]
+Get:4 http://ftp.debian-ports.org unreleased InRelease [40.8 kB]
+Get:5 http://incoming.debian-ports.org unstable Release [43.8 kB]
+Get:6 http://ftp.debian.org unstable/main Sources/DiffIndex [27.9 kB]
+Get:7 http://ftp.debian-ports.org unstable/main m68k Packages [14.9 MB]
+Get:8 http://incoming.debian.org buildd-unstable/main Sources [172 kB]
+Get:9 http://incoming.debian-ports.org unstable/main m68k Packages [43.4 kB]
+Ign http://incoming.debian-ports.org unstable/main Translation-en
+Get:10 http://ftp.debian-ports.org unreleased/main m68k Packages [29.8 kB]
+Ign http://ftp.debian-ports.org unstable/main Translation-en
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Fetched 15.4 MB in 11min 1s (23.3 kB/s)
+Reading package lists...
+E: Write error - write (28: No space left on device)
+E: IO Error saving source cache
+E: The package lists or status file could not be parsed or opened.
+
++------------------------------------------------------------------------------+
+| Fetch source files |
++------------------------------------------------------------------------------+
+
+
+Check APT
+---------
+
+Checking available source versions...
+
+Download source files with APT
+------------------------------
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 4332 kB of source archives.
+Get:1 http://ftp.debian.org/debian/ unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://ftp.debian.org/debian/ unstable/main samtools 1.2-4 (tar) [4319 kB]
+Err http://ftp.debian.org/debian/ unstable/main samtools 1.2-4 (tar)
+ Error writing to output file - write (28: No space left on device) [IP: 130.89.148.12 80]
+Err http://ftp.debian.org/debian/ unstable/main samtools 1.2-4 (diff)
+ Bad header line [IP: 130.89.148.12 80]
+Fetched 2116 B in 9s (223 B/s)
+E: Failed to fetch http://ftp.debian.org/debian/pool/main/s/samtools/samtools_1.2.orig.tar.gz Error writing to output file - write (28: No space left on device) [IP: 130.89.148.12 80]
+
+E: Failed to fetch http://ftp.debian.org/debian/pool/main/s/samtools/samtools_1.2-4.debian.tar.xz Bad header line [IP: 130.89.148.12 80]
+
+E: Failed to fetch some archives.
+apt-get for sources failed
+
++------------------------------------------------------------------------------+
+| Cleanup |
++------------------------------------------------------------------------------+
+
+Not cleaning session: cloned chroot in use
+E: Failed to fetch source files
+
++------------------------------------------------------------------------------+
+| Summary |
++------------------------------------------------------------------------------+
+
+Build Architecture: m68k
+Build-Space: 0
+Build-Time: 0
+Distribution: sid
+Fail-Stage: fetch-src
+Host Architecture: m68k
+Install-Time: 0
+Job: samtools_1.2-4
+Machine Architecture: m68k
+Package: samtools
+Package-Time: 0
+Source-Version: 1.2-4
+Space: 0
+Status: failed
+Version: 1.2-4
+--------------------------------------------------------------------------------
+Finished at 20160119-2130
+Build needed 00:00:00, 0k disc space
diff --git a/mips64el.log b/mips64el.log
index cd3f809..131db2d 100644
--- a/mips64el.log
+++ b/mips64el.log
@@ -1,46 +1,43 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-manda-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on argos.ayous.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (mips64el) 23 Sep 2015 01:48 ║
+║ samtools 1.2-4 (mips64el) 22 Dec 2015 12:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mips64el
Build Architecture: mips64el
-I: NOTICE: Log filtering will replace 'build/samtools-PP85F4/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-PP85F4' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mips64el-sbuild-514192e8-3173-40d8-87da-bf80243c9a40' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-gOUUkg/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-gOUUkg' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mips64el-sbuild-eef44738-cc75-4fa0-bcb9-ec5938b7d505' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org unstable InRelease [253 kB]
-Get:2 http://ftp.de.debian.org unstable InRelease [253 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:4 http://ftp.debian.org unstable/main Sources [8101 kB]
-Get:5 http://ftp.de.debian.org unstable/main Sources [8101 kB]
-Get:6 http://incoming.debian.org buildd-unstable/main Sources [401 kB]
-Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1812 B]
-Get:9 http://incoming.debian.org buildd-unstable/main mips64el Packages [356 kB]
-Get:10 http://incoming.debian.org buildd-unstable/contrib mips64el Packages [1216 B]
-Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:13 http://ftp.debian.org unstable/main mips64el Packages [5969 kB]
-Get:14 http://ftp.de.debian.org unstable/contrib Sources [59.7 kB]
-Get:15 http://ftp.de.debian.org unstable/non-free Sources [106 kB]
-Get:16 http://ftp.de.debian.org unstable/main mips64el Packages [5969 kB]
-Get:17 http://ftp.debian.org unstable/contrib mips64el Packages [28.0 kB]
-Get:18 http://ftp.de.debian.org unstable/contrib mips64el Packages [28.0 kB]
-Fetched 29.9 MB in 31s (940 kB/s)
+Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:2 http://mirror.ayous.org/debian unstable InRelease [265 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://mirror.ayous.org/debian unstable/main Sources [8422 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [8422 kB]
+Get:6 http://mirror.ayous.org/debian unstable/main mips64el Packages [7533 kB]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [181 kB]
+Get:8 http://mirror.ayous.org/debian unstable/contrib mips64el Packages [44.4 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/main mips64el Packages [195 kB]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mips64el Packages [568 B]
+Get:13 http://ftp.debian.org/debian unstable/main mips64el Packages [7533 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib mips64el Packages [44.4 kB]
+Fetched 33.0 MB in 52s (630 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +57,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 0s (6235 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://mirror.ayous.org/debian unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://mirror.ayous.org/debian unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://mirror.ayous.org/debian unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 12s (353 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +78,18 @@ 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-iDYCuv/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-GhBar7/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]
+Get:1 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ Packages [526 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +102,31 @@ Building dependency tree...
Reading state information...
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 11 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 0 B/772 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-GhBar7/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
+debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 15%
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(Reading database ... 25%
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(Reading database ... 40%
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(Reading database ... 50%
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(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 ... 11696 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
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(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 ... 12321 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: 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: 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)
-dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-iUt9l7/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Filtered Build-Depends: 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-1hx1zM/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]
+Get:1 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Sources [361 B]
+Get:5 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ Packages [619 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,73 +137,78 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 11 not upgraded.
-Need to get 18.0 MB/18.0 MB of archives.
-After this operation, 69.1 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main libmagic1 mips64el 1:5.25-2 [255 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main groff-base mips64el 1.22.3-1+b1 [1279 kB]
-Get:4 http://incoming.debian.org/debian-buildd/ buildd-unstable/main file mips64el 1:5.25-2 [61.9 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips64el 9.0.6+b1 [188 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips64el 1.4.1-1+b1 [26.7 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main man-db mips64el 2.7.3-1 [988 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libffi6 mips64el 3.2.1-3+b1 [20.8 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips64el 0.19.6-1 [122 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libicu55 mips64el 55.1-5 [7580 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips64el 2.9.2+zdfsg1-4 [826 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips64el 2.44.1-1.1+b1 [2305 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips64el 0.6.8-3+b1 [123 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips64el 0.9.3-5.2+b1 [258 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext mips64el 0.19.6-1 [1426 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libhts1 mips64el 1.2.1-1 [213 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main libhts-dev mips64el 1.2.1-1 [303 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main libio-pty-perl mips64el 1:1.08-1 [33.2 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev mips64el 6.0+20150810-1+b1 [83.8 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev mips64el 6.0+20150810-1+b1 [182 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main tabix mips64el 1.2.1-1 [225 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips64el 1:1.2.8.dfsg-2+b1 [205 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 5 not upgraded.
+Need to get 18.3 MB/18.3 MB of archives.
+After this operation, 69.7 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-1hx1zM/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [872 B]
+Get:2 http://mirror.ayous.org/debian unstable/main mips64el bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://mirror.ayous.org/debian unstable/main mips64el groff-base mips64el 1.22.3-4 [1280 kB]
+Get:4 http://mirror.ayous.org/debian unstable/main mips64el bsdmainutils mips64el 9.0.6+b2 [188 kB]
+Get:5 http://mirror.ayous.org/debian unstable/main mips64el libpipeline1 mips64el 1.4.1-1+b1 [26.7 kB]
+Get:6 http://mirror.ayous.org/debian unstable/main mips64el man-db mips64el 2.7.5-1 [990 kB]
+Get:7 http://mirror.ayous.org/debian unstable/main mips64el libmagic1 mips64el 1:5.25-2 [255 kB]
+Get:8 http://mirror.ayous.org/debian unstable/main mips64el file mips64el 1:5.25-2 [61.9 kB]
+Get:9 http://mirror.ayous.org/debian unstable/main mips64el gettext-base mips64el 0.19.6-1 [122 kB]
+Get:10 http://mirror.ayous.org/debian unstable/main mips64el libicu55 mips64el 55.1-6 [7573 kB]
+Get:11 http://mirror.ayous.org/debian unstable/main mips64el libxml2 mips64el 2.9.3+dfsg1-1 [830 kB]
+Get:12 http://mirror.ayous.org/debian unstable/main mips64el libffi6 mips64el 3.2.1-4 [20.7 kB]
+Get:13 http://mirror.ayous.org/debian unstable/main mips64el libglib2.0-0 mips64el 2.46.2-1 [2481 kB]
+Get:14 http://mirror.ayous.org/debian unstable/main mips64el libcroco3 mips64el 0.6.11-1 [131 kB]
+Get:15 http://mirror.ayous.org/debian unstable/main mips64el libunistring0 mips64el 0.9.3-5.2+b1 [258 kB]
+Get:16 http://mirror.ayous.org/debian unstable/main mips64el gettext mips64el 0.19.6-1 [1426 kB]
+Get:17 http://mirror.ayous.org/debian unstable/main mips64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://mirror.ayous.org/debian unstable/main mips64el po-debconf all 1.0.18 [248 kB]
+Get:19 http://mirror.ayous.org/debian unstable/main mips64el libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://mirror.ayous.org/debian unstable/main mips64el libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://mirror.ayous.org/debian unstable/main mips64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://mirror.ayous.org/debian unstable/main mips64el dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://mirror.ayous.org/debian unstable/main mips64el debhelper all 9.20151220 [830 kB]
+Get:24 http://mirror.ayous.org/debian unstable/main mips64el libhts1 mips64el 1.2.1-2 [212 kB]
+Get:25 http://mirror.ayous.org/debian unstable/main mips64el libhts-dev mips64el 1.2.1-2 [302 kB]
+Get:26 http://mirror.ayous.org/debian unstable/main mips64el libio-pty-perl mips64el 1:1.08-1.1+b1 [31.6 kB]
+Get:27 http://mirror.ayous.org/debian unstable/main mips64el libtinfo-dev mips64el 6.0+20151024-2 [83.5 kB]
+Get:28 http://mirror.ayous.org/debian unstable/main mips64el libncurses5-dev mips64el 6.0+20151024-2 [184 kB]
+Get:29 http://mirror.ayous.org/debian unstable/main mips64el tabix mips64el 1.2.1-2 [224 kB]
+Get:30 http://mirror.ayous.org/debian unstable/main mips64el zlib1g-dev mips64el 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.0 MB in 3s (5872 kB/s)
+Fetched 18.3 MB in 2s (6759 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 ... 11696 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
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(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 ... 12321 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+b1_mips64el.deb ...
-Unpacking groff-base (1.22.3-1+b1) ...
+Preparing to unpack .../groff-base_1.22.3-4_mips64el.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_mips64el.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b2_mips64el.deb ...
+Unpacking bsdmainutils (9.0.6+b2) ...
Selecting previously unselected package libpipeline1:mips64el.
Preparing to unpack .../libpipeline1_1.4.1-1+b1_mips64el.deb ...
Unpacking libpipeline1:mips64el (1.4.1-1+b1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_mips64el.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:mips64el.
-Preparing to unpack .../libffi6_3.2.1-3+b1_mips64el.deb ...
-Unpacking libffi6:mips64el (3.2.1-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_mips64el.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libmagic1:mips64el.
Preparing to unpack .../libmagic1_1%3a5.25-2_mips64el.deb ...
Unpacking libmagic1:mips64el (1:5.25-2) ...
@@ -200,17 +219,20 @@ Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_mips64el.deb ...
Unpacking gettext-base (0.19.6-1) ...
Selecting previously unselected package libicu55:mips64el.
-Preparing to unpack .../libicu55_55.1-5_mips64el.deb ...
-Unpacking libicu55:mips64el (55.1-5) ...
+Preparing to unpack .../libicu55_55.1-6_mips64el.deb ...
+Unpacking libicu55:mips64el (55.1-6) ...
Selecting previously unselected package libxml2:mips64el.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_mips64el.deb ...
-Unpacking libxml2:mips64el (2.9.2+zdfsg1-4) ...
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_mips64el.deb ...
+Unpacking libxml2:mips64el (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:mips64el.
+Preparing to unpack .../libffi6_3.2.1-4_mips64el.deb ...
+Unpacking libffi6:mips64el (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:mips64el.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1+b1_mips64el.deb ...
-Unpacking libglib2.0-0:mips64el (2.44.1-1.1+b1) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-1_mips64el.deb ...
+Unpacking libglib2.0-0:mips64el (2.46.2-1) ...
Selecting previously unselected package libcroco3:mips64el.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_mips64el.deb ...
-Unpacking libcroco3:mips64el (0.6.8-3+b1) ...
+Preparing to unpack .../libcroco3_0.6.11-1_mips64el.deb ...
+Unpacking libcroco3:mips64el (0.6.11-1) ...
Selecting previously unselected package libunistring0:mips64el.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_mips64el.deb ...
Unpacking libunistring0:mips64el (0.9.3-5.2+b1) ...
@@ -223,72 +245,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:mips64el.
-Preparing to unpack .../libhts1_1.2.1-1_mips64el.deb ...
-Unpacking libhts1:mips64el (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_mips64el.deb ...
+Unpacking libhts1:mips64el (1.2.1-2) ...
Selecting previously unselected package libhts-dev:mips64el.
-Preparing to unpack .../libhts-dev_1.2.1-1_mips64el.deb ...
-Unpacking libhts-dev:mips64el (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_mips64el.deb ...
+Unpacking libhts-dev:mips64el (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1_mips64el.deb ...
-Unpacking libio-pty-perl (1:1.08-1) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_mips64el.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:mips64el.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1+b1_mips64el.deb ...
-Unpacking libtinfo-dev:mips64el (6.0+20150810-1+b1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_mips64el.deb ...
+Unpacking libtinfo-dev:mips64el (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:mips64el.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1+b1_mips64el.deb ...
-Unpacking libncurses5-dev:mips64el (6.0+20150810-1+b1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_mips64el.deb ...
+Unpacking libncurses5-dev:mips64el (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_mips64el.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_mips64el.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:mips64el.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_mips64el.deb ...
Unpacking zlib1g-dev:mips64el (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1+b1) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b2) ...
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 libpipeline1:mips64el (1.4.1-1+b1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:mips64el (3.2.1-3+b1) ...
Setting up libmagic1:mips64el (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
-Setting up libicu55:mips64el (55.1-5) ...
-Setting up libxml2:mips64el (2.9.2+zdfsg1-4) ...
-Setting up libglib2.0-0:mips64el (2.44.1-1.1+b1) ...
+Setting up libicu55:mips64el (55.1-6) ...
+Setting up libxml2:mips64el (2.9.3+dfsg1-1) ...
+Setting up libffi6:mips64el (3.2.1-4) ...
+Setting up libglib2.0-0:mips64el (2.46.2-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:mips64el (0.6.8-3+b1) ...
+Setting up libcroco3:mips64el (0.6.11-1) ...
Setting up libunistring0:mips64el (0.9.3-5.2+b1) ...
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 (9.20150811) ...
-Setting up libhts1:mips64el (1.2.1-1) ...
-Setting up libhts-dev:mips64el (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1) ...
-Setting up libtinfo-dev:mips64el (6.0+20150810-1+b1) ...
-Setting up libncurses5-dev:mips64el (6.0+20150810-1+b1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:mips64el (1.2.1-2) ...
+Setting up libhts-dev:mips64el (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:mips64el (6.0+20151024-2) ...
+Setting up libncurses5-dev:mips64el (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:mips64el (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 4.1.0-0.bpo.1-loongson-3 mipsel (mips64)
-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+b1 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8+b1 coreutils_8.23-4+b1 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 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2+b1 dpkg-dev_1.18.2 e2fslibs_1.42.13-1+b1 e2fspro [...]
+Kernel: Linux 4.1.0-0.bpo.2-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-3 gcc-5_5.3.1-3 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-3 libstdc++6_5.3.1-3 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38+b1 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b2 bsdutils_1:2.27.1-1 build-essential_12.1+b1 bzip2_1.0.6-8+b1 coreutils_8.23-4+b1 cpp_4:5.3.1-1 cpp-5_5.3.1-3 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debfoster_2.7-2 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1+b1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.104- [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +339,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -317,17 +358,17 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=5
+DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-mips64el-sbuild
SCHROOT_CHROOT_NAME=sid-mips64el-sbuild
SCHROOT_COMMAND=env
-SCHROOT_GID=1009
+SCHROOT_GID=802
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mips64el-sbuild-514192e8-3173-40d8-87da-bf80243c9a40
-SCHROOT_UID=2952
+SCHROOT_SESSION_ID=sid-mips64el-sbuild-eef44738-cc75-4fa0-bcb9-ec5938b7d505
+SCHROOT_UID=802
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
@@ -336,7 +377,7 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture mips64el
@@ -345,7 +386,7 @@ dpkg-source: info: using options from samtools-1.2/debian/source/options: --sing
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
- make -j5 distclean
+ make -j4 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
@@ -385,7 +426,7 @@ dh_auto_build -- \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j5 HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
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_index.o bam_index.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_plcmd.o bam_plcmd.c
@@ -453,15 +494,15 @@ gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
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/mips64el-linux-gnuabi64/libhts.a -lhts -lcurse [...]
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
@@ -471,85 +512,85 @@ dh_auto_test -- \
HTSDIR="/usr/include" \
HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j5 test HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/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/Ps_M93HaPJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/eHILIcLGar/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Ps_M93HaPJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/eHILIcLGar/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Ps_M93HaPJ/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/eHILIcLGar/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/Ps_M93HaPJ/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/eHILIcLGar/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/Ps_M93HaPJ/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/eHILIcLGar/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/Ps_M93HaPJ/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/eHILIcLGar/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/Ps_M93HaPJ/mpileup.bam.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/eHILIcLGar/mpileup.bam.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Ps_M93HaPJ/mpileup.bam.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/eHILIcLGar/mpileup.bam.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/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/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/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/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/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/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/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/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ps_M93HaPJ/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eHILIcLGar/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ps_M93HaPJ/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:1050-1060 /tmp/eHILIcLGar/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +820,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/eHILIcLGar/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/eHILIcLGar/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/eHILIcLGar/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/eHILIcLGar/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/eHILIcLGar/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/eHILIcLGar/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.test067.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/eHILIcLGar/view.test067.sam -h -l Library 2 /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.test069.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/eHILIcLGar/view.test069.sam -h -l Library 2 /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.test071.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/eHILIcLGar/view.test071.sam -h -l Library 2 /tmp/eHILIcLGar/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/Ps_M93HaPJ/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/eHILIcLGar/view.test006.cram
.. expected failure
@@ -1299,82 +1340,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/Ps_M93HaPJ/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/eHILIcLGar/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/Ps_M93HaPJ/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/eHILIcLGar/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/Ps_M93HaPJ/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/eHILIcLGar/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/Ps_M93HaPJ/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/eHILIcLGar/depad.001p.bam
.. expected failure
@@ -1412,7 +1453,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/sKujszcdjm - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/YKE3bspd73 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1461,23 +1502,358 @@ Samtools mpileup tests:
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
-E: Caught signal ‘Terminated’: terminating immediately
-make[1]: *** wait: No child processes. Stop.
-make[1]: *** Waiting for unfinished jobs....
-make: *** wait: No child processes. Stop.
-make[1]: *** wait: No child processes. Stop.
-make[2]: *** [test] Terminated
-make: *** Waiting for unfinished jobs....
-make: *** wait: No child processes. Stop.
-Makefile:182: recipe for target 'test' failed
-Build killed with signal TERM after 150 minutes of inactivity
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a
+ install -d debian/samtools
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+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»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ 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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
+ dh_installdocs -a -O--parallel
+ 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 -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
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ cd '/«PKGBUILDDIR»'
+ dh_fixperms -a -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 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/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/usr/lib/mips64el-linux-gnuabi64/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ 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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/07
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/07/34737a71531453cd592ac8193ae73a750fe594.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/07/34737a71531453cd592ac8193ae73a750fe594.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/07/34737a71531453cd592ac8193ae73a750fe594.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/11b027dedaee42cb9f779e10395f1c296cebbb.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/11b027dedaee42cb9f779e10395f1c296cebbb.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/11b027dedaee42cb9f779e10395f1c296cebbb.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c9/a4a02eada81ed96efa15d1b42d5cc861ec9adf.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c9/a4a02eada81ed96efa15d1b42d5cc861ec9adf.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/c9/a4a02eada81ed96efa15d1b42d5cc861ec9adf.debug debian/samtools/usr/bin/md5fa
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/87519580c7b6aff87d9a2f4a0d3f11e7ef996f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/87519580c7b6aff87d9a2f4a0d3f11e7ef996f.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/5a/87519580c7b6aff87d9a2f4a0d3f11e7ef996f.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/34
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/34/fb385678bf09f78315c2a0d04df6df5a7a5323.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/34/fb385678bf09f78315c2a0d04df6df5a7a5323.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/34/fb385678bf09f78315c2a0d04df6df5a7a5323.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/40fe28753166d979c8f22ae5cc2bb11733efaa.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/40fe28753166d979c8f22ae5cc2bb11733efaa.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/92/40fe28753166d979c8f22ae5cc2bb11733efaa.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/f8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/f8/0e865297a1039ba66d31313f6d18554742907d.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/f8/0e865297a1039ba66d31313f6d18554742907d.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/f8/0e865297a1039ba66d31313f6d18554742907d.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=0734737a71531453cd592ac8193ae73a750fe594 34fb385678bf09f78315c2a0d04df6df5a7a5323 5a11b027dedaee42cb9f779e10395f1c29 [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ 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 0644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -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 0644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_mips64el.deb'.
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_mips64el.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (argos) <buildd_mipsel-argos at buildd.debian.org> >../samtools_1.2-4_mips64el.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150923-0444
+Build finished at 20151222-1334
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-4_mips64el.changes:
+────────────────────────────────
+
+Format: 1.8
+Date: Mon, 21 Dec 2015 13:49:05 +0100
+Source: samtools
+Binary: samtools samtools-test
+Architecture: mips64el
+Version: 1.2-4
+Distribution: sid
+Urgency: medium
+Maintainer: mipsel Build Daemon (argos) <buildd_mipsel-argos at buildd.debian.org>
+Changed-By: Andreas Tille <tille at debian.org>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
+Changes:
+ samtools (1.2-4) unstable; urgency=medium
+ .
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
+Checksums-Sha1:
+ 2c16ce78ce7ea7576e4845d50e19810af72e3382 415882 samtools-dbgsym_1.2-4_mips64el.deb
+ b96464a027cb864b1d01b4c783eb07631f5af614 387522 samtools_1.2-4_mips64el.deb
+Checksums-Sha256:
+ 7ce3a5d812177fc3dd1ef99cbbc4e27837900cf2c263fa61bc3fb14b460fe274 415882 samtools-dbgsym_1.2-4_mips64el.deb
+ 34f8720f0b783d5877b09ed70043a857f7aa5ed5df5c697821e23e48a0017a7e 387522 samtools_1.2-4_mips64el.deb
+Files:
+ d1a1b925ba4cc7c025f9b259f7f62445 415882 debug extra samtools-dbgsym_1.2-4_mips64el.deb
+ 4faabfad6e673e624081417c50f3a4ac 387522 science optional samtools_1.2-4_mips64el.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-dbgsym_1.2-4_mips64el.deb
+──────────────────────────────────
+
+ new debian package, version 2.0.
+ size 415882 bytes: control archive=822 bytes.
+ 650 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: mips64el
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1482
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 0734737a71531453cd592ac8193ae73a750fe594 34fb385678bf09f78315c2a0d04df6df5a7a5323 5a11b027dedaee42cb9f779e10395f1c296cebbb 5a87519580c7b6aff87d9a2f4a0d3f11e7ef996f 9240fe28753166d979c8f22ae5cc2bb11733efaa c9a4a02eada81ed96efa15d1b42d5cc861ec9adf f80e865297a1039ba66d31313f6d18554742907d
+
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/07/
+-rw-r--r-- root/root 49792 2015-12-22 13:33 ./usr/lib/debug/.build-id/07/34737a71531453cd592ac8193ae73a750fe594.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/34/
+-rw-r--r-- root/root 20288 2015-12-22 13:33 ./usr/lib/debug/.build-id/34/fb385678bf09f78315c2a0d04df6df5a7a5323.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/5a/
+-rw-r--r-- root/root 20456 2015-12-22 13:33 ./usr/lib/debug/.build-id/5a/11b027dedaee42cb9f779e10395f1c296cebbb.debug
+-rw-r--r-- root/root 20280 2015-12-22 13:33 ./usr/lib/debug/.build-id/5a/87519580c7b6aff87d9a2f4a0d3f11e7ef996f.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/92/
+-rw-r--r-- root/root 38024 2015-12-22 13:33 ./usr/lib/debug/.build-id/92/40fe28753166d979c8f22ae5cc2bb11733efaa.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/c9/
+-rw-r--r-- root/root 27048 2015-12-22 13:33 ./usr/lib/debug/.build-id/c9/a4a02eada81ed96efa15d1b42d5cc861ec9adf.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/lib/debug/.build-id/f8/
+-rw-r--r-- root/root 1323552 2015-12-22 13:33 ./usr/lib/debug/.build-id/f8/0e865297a1039ba66d31313f6d18554742907d.debug
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-22 13:33 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_mips64el.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 387522 bytes: control archive=1610 bytes.
+ 811 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
+ Package: samtools
+ Version: 1.2-4
+ Architecture: mips64el
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1219
+ Depends: libc6 (>= 2.21), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ one 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 2015-12-22 13:33 ./
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/bin/
+-rwxr-xr-x root/root 23336 2015-12-22 13:33 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 11080 2015-12-22 13:33 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 11080 2015-12-22 13:33 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 19360 2015-12-22 13:33 ./usr/bin/md5fa
+-rwxr-xr-x root/root 15168 2015-12-22 13:33 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 935296 2015-12-22 13:33 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 36184 2015-12-22 13:33 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-22 13:33 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-22 13:33 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-22 13:33 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-22 13:33 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-22 13:33 ./usr/share/man/man1/wgsim.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1491,20 +1867,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mips64el
-Build-Space: 57712
-Build-Time: 10385
+Build-Space: 21348
+Build-Time: 3297
Distribution: sid
-Fail-Stage: build
Host Architecture: mips64el
-Install-Time: 57
-Job: samtools_1.2-3
+Install-Time: 68
+Job: samtools_1.2-4
Machine Architecture: mipsel
Package: samtools
-Package-Time: 10531
-Source-Version: 1.2-3
-Space: 57712
-Status: attempted
-Version: 1.2-3
+Package-Time: 3496
+Source-Version: 1.2-4
+Space: 21348
+Status: successful
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150923-0444
-Build needed 02:55:31, 57712k disc space
+Finished at 20151222-1334
+Build needed 00:58:16, 21348k disc space
diff --git a/mipsel.log b/mipsel.log
index b9ae932..f179514 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,46 +1,47 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-aql-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-manda-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (mipsel) 22 Sep 2015 16:19 ║
+║ samtools 1.2-4 (mipsel) 21 Dec 2015 13:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mipsel
Build Architecture: mipsel
-I: NOTICE: Log filtering will replace 'build/samtools-B_M8Do/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-B_M8Do' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-af2c7f8d-0e84-4285-9965-6f83ee9596f6' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-E4xeEx/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-E4xeEx' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-9e652671-aee1-4cf5-8e07-388c5b6c3a4d' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.uk.debian.org unstable InRelease [253 kB]
-Get:2 http://ftp.debian.org unstable InRelease [253 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:4 http://incoming.debian.org buildd-unstable/main Sources [354 kB]
-Get:5 http://ftp.uk.debian.org unstable/main Sources [8093 kB]
-Get:6 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:7 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
-Get:8 http://incoming.debian.org buildd-unstable/main mipsel Packages [98.7 kB]
-Get:9 http://incoming.debian.org buildd-unstable/contrib mipsel Packages [1060 B]
-Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:13 http://ftp.uk.debian.org unstable/contrib Sources [59.7 kB]
-Get:14 http://ftp.uk.debian.org unstable/non-free Sources [106 kB]
-Get:15 http://ftp.debian.org unstable/main mipsel Packages [7352 kB]
-Get:16 http://ftp.uk.debian.org unstable/main mipsel Packages [7352 kB]
-Get:17 http://ftp.debian.org unstable/contrib mipsel Packages [44.3 kB]
-Get:18 http://ftp.uk.debian.org unstable/contrib mipsel Packages [44.3 kB]
-Fetched 32.4 MB in 49s (648 kB/s)
+Get:1 http://ftp.de.debian.org/debian unstable InRelease [265 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [203 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/main mipsel Packages [198 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mipsel Packages [568 B]
+Get:9 http://ftp.de.debian.org/debian unstable/main Sources [8421 kB]
+Get:10 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/non-free Sources [105 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main mipsel Packages [7786 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:15 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:16 http://ftp.debian.org/debian unstable/main mipsel Packages [7786 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/contrib mipsel Packages [46.9 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib mipsel Packages [46.9 kB]
+Fetched 33.9 MB in 19s (1706 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 0s (4824 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 0s (8561 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-MvnuoI/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-v1gSqC/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]
+Get:1 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ Packages [527 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
-Need to get 0 B/768 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 12 not upgraded.
+Need to get 0 B/770 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-v1gSqC/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(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 ... 11666 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
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(Reading database ... 60%
(Reading database ... 65%
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(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12076 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-RPeFbc/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-llH8qF/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]
+Get:1 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ Packages [734 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 17.8 MB/17.8 MB of archives.
-After this operation, 66.5 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base mipsel 1.22.3-1 [1218 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils mipsel 9.0.6 [184 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 mipsel 1.4.1-1 [26.9 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db mipsel 2.7.3-1 [988 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi6 mipsel 3.2.1-3 [18.4 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.44.1-1.1 [2294 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libicu55 mipsel 55.1-5 [7567 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 mipsel 2.9.2+zdfsg1-4 [824 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.8-3+b1 [119 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 mipsel 1:5.25-1 [258 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main file mipsel 1:5.25-1 [61.6 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext-base mipsel 0.19.6-1 [120 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext mipsel 0.19.6-1 [1413 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libhts1 mipsel 1.2.1-1 [211 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev mipsel 1.2.1-1 [291 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main libio-pty-perl mipsel 1:1.08-1+b4 [33.6 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev mipsel 6.0+20150810-1 [78.5 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev mipsel 6.0+20150810-1 [173 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main tabix mipsel 1.2.1-1 [220 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.8.dfsg-2+b1 [205 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 12 not upgraded.
+Need to get 18.3 MB/18.3 MB of archives.
+After this operation, 67.3 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-llH8qF/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [978 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main mipsel bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.de.debian.org/debian unstable/main mipsel groff-base mipsel 1.22.3-4 [1275 kB]
+Get:4 http://ftp.de.debian.org/debian unstable/main mipsel bsdmainutils mipsel 9.0.6+b1 [185 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main mipsel libpipeline1 mipsel 1.4.1-1 [26.9 kB]
+Get:6 http://ftp.de.debian.org/debian unstable/main mipsel man-db mipsel 2.7.5-1 [991 kB]
+Get:7 http://ftp.de.debian.org/debian unstable/main mipsel libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main mipsel libmagic1 mipsel 1:5.25-2 [258 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main mipsel file mipsel 1:5.25-2 [61.6 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/main mipsel gettext-base mipsel 0.19.6-1 [120 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/main mipsel libicu55 mipsel 55.1-6 [7586 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/main mipsel libxml2 mipsel 2.9.3+dfsg1-1 [829 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main mipsel libffi6 mipsel 3.2.1-4 [18.6 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main mipsel libglib2.0-0 mipsel 2.46.2-1 [2500 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main mipsel libcroco3 mipsel 0.6.11-1 [131 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main mipsel gettext mipsel 0.19.6-1 [1413 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main mipsel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main mipsel po-debconf all 1.0.18 [248 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main mipsel libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main mipsel libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main mipsel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main mipsel dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://ftp.de.debian.org/debian unstable/main mipsel debhelper all 9.20151220 [830 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main mipsel libhts1 mipsel 1.2.1-2 [214 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main mipsel libhts-dev mipsel 1.2.1-2 [295 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main mipsel libio-pty-perl mipsel 1:1.08-1.1+b1 [31.5 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main mipsel libtinfo-dev mipsel 6.0+20151024-2 [78.8 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main mipsel libncurses5-dev mipsel 6.0+20151024-2 [177 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main mipsel tabix mipsel 1.2.1-2 [216 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main mipsel zlib1g-dev mipsel 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.8 MB in 3s (4600 kB/s)
+Fetched 18.3 MB in 1s (10.0 MB/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 ... 11666 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 30%
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(Reading database ... 40%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12076 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_mipsel.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_mipsel.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_mipsel.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_mipsel.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:mipsel.
Preparing to unpack .../libpipeline1_1.4.1-1_mipsel.deb ...
Unpacking libpipeline1:mipsel (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_mipsel.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:mipsel.
-Preparing to unpack .../libffi6_3.2.1-3_mipsel.deb ...
-Unpacking libffi6:mipsel (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:mipsel.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_mipsel.deb ...
-Unpacking libglib2.0-0:mipsel (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:mipsel.
-Preparing to unpack .../libicu55_55.1-5_mipsel.deb ...
-Unpacking libicu55:mipsel (55.1-5) ...
-Selecting previously unselected package libxml2:mipsel.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_mipsel.deb ...
-Unpacking libxml2:mipsel (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:mipsel.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_mipsel.deb ...
-Unpacking libcroco3:mipsel (0.6.8-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_mipsel.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:mipsel.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_mipsel.deb ...
Unpacking libunistring0:mipsel (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:mipsel.
-Preparing to unpack .../libmagic1_1%3a5.25-1_mipsel.deb ...
-Unpacking libmagic1:mipsel (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_mipsel.deb ...
+Unpacking libmagic1:mipsel (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_mipsel.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_mipsel.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_mipsel.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:mipsel.
+Preparing to unpack .../libicu55_55.1-6_mipsel.deb ...
+Unpacking libicu55:mipsel (55.1-6) ...
+Selecting previously unselected package libxml2:mipsel.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_mipsel.deb ...
+Unpacking libxml2:mipsel (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:mipsel.
+Preparing to unpack .../libffi6_3.2.1-4_mipsel.deb ...
+Unpacking libffi6:mipsel (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:mipsel.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_mipsel.deb ...
+Unpacking libglib2.0-0:mipsel (2.46.2-1) ...
+Selecting previously unselected package libcroco3:mipsel.
+Preparing to unpack .../libcroco3_0.6.11-1_mipsel.deb ...
+Unpacking libcroco3:mipsel (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_mipsel.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:mipsel.
-Preparing to unpack .../libhts1_1.2.1-1_mipsel.deb ...
-Unpacking libhts1:mipsel (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_mipsel.deb ...
+Unpacking libhts1:mipsel (1.2.1-2) ...
Selecting previously unselected package libhts-dev:mipsel.
-Preparing to unpack .../libhts-dev_1.2.1-1_mipsel.deb ...
-Unpacking libhts-dev:mipsel (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_mipsel.deb ...
+Unpacking libhts-dev:mipsel (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_mipsel.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_mipsel.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:mipsel.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_mipsel.deb ...
-Unpacking libtinfo-dev:mipsel (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_mipsel.deb ...
+Unpacking libtinfo-dev:mipsel (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:mipsel.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_mipsel.deb ...
-Unpacking libncurses5-dev:mipsel (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_mipsel.deb ...
+Unpacking libncurses5-dev:mipsel (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_mipsel.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_mipsel.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:mipsel.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_mipsel.deb ...
Unpacking zlib1g-dev:mipsel (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:mipsel (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:mipsel (3.2.1-3) ...
-Setting up libglib2.0-0:mipsel (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:mipsel (55.1-5) ...
-Setting up libxml2:mipsel (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:mipsel (0.6.8-3+b1) ...
Setting up libunistring0:mipsel (0.9.3-5.2+b1) ...
-Setting up libmagic1:mipsel (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:mipsel (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:mipsel (55.1-6) ...
+Setting up libxml2:mipsel (2.9.3+dfsg1-1) ...
+Setting up libffi6:mipsel (3.2.1-4) ...
+Setting up libglib2.0-0:mipsel (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:mipsel (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:mipsel (1.2.1-1) ...
-Setting up libhts-dev:mipsel (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:mipsel (6.0+20150810-1) ...
-Setting up libncurses5-dev:mipsel (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:mipsel (1.2.1-2) ...
+Setting up libhts-dev:mipsel (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:mipsel (6.0+20151024-2) ...
+Setting up libncurses5-dev:mipsel (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16.0-4-loongson-3 mipsel (mips64)
-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_1:2.27-3 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 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_1.42.13-1 faker [...]
+Kernel: Linux 4.1.0-0.bpo.1-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-3 gcc-5_5.3.1-3 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-3 libstdc++6_5.3.1-3 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-3 dash_0.5.7-4+b1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -326,18 +371,19 @@ SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mipsel-sbuild-af2c7f8d-0e84-4285-9965-6f83ee9596f6
+SCHROOT_SESSION_ID=sid-mipsel-sbuild-9e652671-aee1-4cf5-8e07-388c5b6c3a4d
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
USERNAME=buildd
+XDG_SESSION_ID=c112
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture mipsel
@@ -454,16 +500,16 @@ gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
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/mipsel-linux-gnu/libhts.a -lhts -lcurses -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -475,82 +521,82 @@ dh_auto_test -- \
make -j5 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-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/xlCscIPJVB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/NhyY4wH34k/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/xlCscIPJVB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NhyY4wH34k/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/xlCscIPJVB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NhyY4wH34k/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/xlCscIPJVB/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/NhyY4wH34k/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/xlCscIPJVB/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/NhyY4wH34k/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/xlCscIPJVB/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/NhyY4wH34k/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/xlCscIPJVB/mpileup.bam.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/NhyY4wH34k/mpileup.bam.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xlCscIPJVB/mpileup.bam.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/NhyY4wH34k/mpileup.bam.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/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/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/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/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/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/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/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/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xlCscIPJVB/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NhyY4wH34k/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xlCscIPJVB/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:1050-1060 /tmp/NhyY4wH34k/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -780,80 +826,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/xlCscIPJVB/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/NhyY4wH34k/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/xlCscIPJVB/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/NhyY4wH34k/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/xlCscIPJVB/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/NhyY4wH34k/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/xlCscIPJVB/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/NhyY4wH34k/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/NhyY4wH34k/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/xlCscIPJVB/view.test067.sam -h -l Library 2 /tmp/xlCscIPJVB/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NhyY4wH34k/view.test067.sam -h -l Library 2 /tmp/NhyY4wH34k/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/xlCscIPJVB/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NhyY4wH34k/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/xlCscIPJVB/view.test069.sam -h -l Library 2 /tmp/xlCscIPJVB/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NhyY4wH34k/view.test069.sam -h -l Library 2 /tmp/NhyY4wH34k/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/xlCscIPJVB/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NhyY4wH34k/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/xlCscIPJVB/view.test071.sam -h -l Library 2 /tmp/xlCscIPJVB/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/NhyY4wH34k/view.test071.sam -h -l Library 2 /tmp/NhyY4wH34k/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/xlCscIPJVB/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/NhyY4wH34k/view.test006.cram
.. expected failure
@@ -1300,82 +1346,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/xlCscIPJVB/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/NhyY4wH34k/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/xlCscIPJVB/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/NhyY4wH34k/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/xlCscIPJVB/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/NhyY4wH34k/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/xlCscIPJVB/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/NhyY4wH34k/depad.001p.bam
.. expected failure
@@ -1413,7 +1459,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/t3oRPTRba5 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/BGs1KDNSoU - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1507,6 +1553,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1519,17 +1568,30 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1537,31 +1599,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/mipsel-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/lib/mipsel-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/dc929d16e954a3836a8a8777afac2dd50151f9.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/dc929d16e954a3836a8a8777afac2dd50151f9.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4d/dc929d16e954a3836a8a8777afac2dd50151f9.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ca
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ca/8b9ee943b7d3b88ef9cb81acfde56c3b1678aa.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ca/8b9ee943b7d3b88ef9cb81acfde56c3b1678aa.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ca/8b9ee943b7d3b88ef9cb81acfde56c3b1678aa.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ea
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ea/88d9c356672be8d40406cb8d9ad3135d48ca22.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ea/88d9c356672be8d40406cb8d9ad3135d48ca22.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/ea/88d9c356672be8d40406cb8d9ad3135d48ca22.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/35
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/35/6aa6af9f6f5578128c3b80b7930ffcf5506664.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/35/6aa6af9f6f5578128c3b80b7930ffcf5506664.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/35/6aa6af9f6f5578128c3b80b7930ffcf5506664.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/40
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/40/6f3090a4f5ac8f76df2cfefddf7f2714c89a21.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/40/6f3090a4f5ac8f76df2cfefddf7f2714c89a21.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/40/6f3090a4f5ac8f76df2cfefddf7f2714c89a21.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/cd98f710724de44ba88633cf48a15d08bd081e.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/cd98f710724de44ba88633cf48a15d08bd081e.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/cd98f710724de44ba88633cf48a15d08bd081e.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3d/0a2131fb3dabfae4efb152c4559634c81535fc.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3d/0a2131fb3dabfae4efb152c4559634c81535fc.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3d/0a2131fb3dabfae4efb152c4559634c81535fc.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=356aa6af9f6f5578128c3b80b7930ffcf5506664 3d0a2131fb3dabfae4efb152c4559634c81535fc 406f3090a4f5ac8f76df2cfefddf7f2714 [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1571,16 +1669,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_mipsel.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mipsel-aql-01) <buildd_mipsel-mipsel-aql-01 at buildd.debian.org> >../samtools_1.2-3_mipsel.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mipsel-manda-01) <buildd_mipsel-mipsel-manda-01 at buildd.debian.org> >../samtools_1.2-4_mipsel.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1635
+Build finished at 20151221-1337
Finished
────────
@@ -1597,54 +1701,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_mipsel.changes:
+samtools_1.2-4_mipsel.changes:
──────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: mipsel
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
-Maintainer: mipsel Build Daemon (mipsel-aql-01) <buildd_mipsel-mipsel-aql-01 at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Maintainer: mipsel Build Daemon (mipsel-manda-01) <buildd_mipsel-mipsel-manda-01 at buildd.debian.org>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- e86ec6723297d87264c9410eb8a222ffdfd1febb 372272 samtools_1.2-3_mipsel.deb
+ e6dd76cf045f7ade59e4d44614e6b799586176d7 409544 samtools-dbgsym_1.2-4_mipsel.deb
+ 8ac85d4a56b4f135c0a4c5d13774bc71302ce917 378468 samtools_1.2-4_mipsel.deb
Checksums-Sha256:
- 321d9562ba086da596950b4f184f85d595744fc537b304a6bdcda362c6124569 372272 samtools_1.2-3_mipsel.deb
+ 79dcedf7107e7e78edf4e260f6a6243b9a17e25a89544a196fd14d9a7dbc70ea 409544 samtools-dbgsym_1.2-4_mipsel.deb
+ 7197de1611a41506f56ebfe2cd2f4f0ad1fec52e76b864ea420369e3bafcf1ab 378468 samtools_1.2-4_mipsel.deb
Files:
- 6c290d86fc238668fd7d2ec7c9438260 372272 science optional samtools_1.2-3_mipsel.deb
+ c75f46e25c5611eea273ea399b7736ca 409544 debug extra samtools-dbgsym_1.2-4_mipsel.deb
+ 227df3c390afe5dc1f5e92b240ef98e1 378468 science optional samtools_1.2-4_mipsel.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_mipsel.deb
+samtools-dbgsym_1.2-4_mipsel.deb
+────────────────────────────────
+
+ new debian package, version 2.0.
+ size 409544 bytes: control archive=819 bytes.
+ 647 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 507
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 356aa6af9f6f5578128c3b80b7930ffcf5506664 3d0a2131fb3dabfae4efb152c4559634c81535fc 406f3090a4f5ac8f76df2cfefddf7f2714c89a21 4ddc929d16e954a3836a8a8777afac2dd50151f9 88cd98f710724de44ba88633cf48a15d08bd081e ca8b9ee943b7d3b88ef9cb81acfde56c3b1678aa ea88d9c356672be8d40406cb8d9ad3135d48ca22
+
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/35/
+-rw-r--r-- root/root 10784 2015-12-21 13:37 ./usr/lib/debug/.build-id/35/6aa6af9f6f5578128c3b80b7930ffcf5506664.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/3d/
+-rw-r--r-- root/root 416220 2015-12-21 13:37 ./usr/lib/debug/.build-id/3d/0a2131fb3dabfae4efb152c4559634c81535fc.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/40/
+-rw-r--r-- root/root 10784 2015-12-21 13:37 ./usr/lib/debug/.build-id/40/6f3090a4f5ac8f76df2cfefddf7f2714c89a21.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/4d/
+-rw-r--r-- root/root 18432 2015-12-21 13:37 ./usr/lib/debug/.build-id/4d/dc929d16e954a3836a8a8777afac2dd50151f9.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/88/
+-rw-r--r-- root/root 18928 2015-12-21 13:37 ./usr/lib/debug/.build-id/88/cd98f710724de44ba88633cf48a15d08bd081e.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/ca/
+-rw-r--r-- root/root 10960 2015-12-21 13:37 ./usr/lib/debug/.build-id/ca/8b9ee943b7d3b88ef9cb81acfde56c3b1678aa.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/lib/debug/.build-id/ea/
+-rw-r--r-- root/root 13796 2015-12-21 13:37 ./usr/lib/debug/.build-id/ea/88d9c356672be8d40406cb8d9ad3135d48ca22.debug
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 13:37 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_mipsel.deb
─────────────────────────
new debian package, version 2.0.
- size 372272 bytes: control archive=1488 bytes.
- 804 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 378468 bytes: control archive=1612 bytes.
+ 809 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: mipsel
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1126
+ Installed-Size: 1153
Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1654,44 +1811,51 @@ samtools_1.2-3_mipsel.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 16:34 ./
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/bin/
--rwxr-xr-x root/root 18432 2015-09-22 16:34 ./usr/bin/ace2sam
+ one 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 2015-12-21 13:37 ./
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/bin/
+-rwxr-xr-x root/root 18364 2015-12-21 13:37 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 10256 2015-09-22 16:34 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10256 2015-09-22 16:34 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14448 2015-09-22 16:34 ./usr/bin/md5fa
--rwxr-xr-x root/root 10288 2015-09-22 16:34 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 10192 2015-12-21 13:37 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10192 2015-12-21 13:37 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14388 2015-12-21 13:37 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10220 2015-12-21 13:37 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 873076 2015-09-22 16:34 ./usr/bin/samtools
+-rwxr-xr-x root/root 897996 2015-12-21 13:37 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 22856 2015-09-22 16:34 ./usr/bin/wgsim
+-rwxr-xr-x root/root 22796 2015-12-21 13:37 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 16:34 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 13:37 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 13:37 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 13:37 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 13:37 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 13:37 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1711,23 +1875,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mipsel
-Build-Space: 18748
-Build-Time: 736
+Build-Space: 19908
+Build-Time: 724
Distribution: sid
Host Architecture: mipsel
-Install-Time: 69
-Job: samtools_1.2-3
+Install-Time: 71
+Job: samtools_1.2-4
Machine Architecture: mipsel
Package: samtools
-Package-Time: 916
-Source-Version: 1.2-3
-Space: 18748
+Package-Time: 877
+Source-Version: 1.2-4
+Space: 19908
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1635
-Build needed 00:15:16, 18748k disc space
-Signature with key 'C1629605' requested:
- signfile /home/buildd/build/samtools_1.2-3_mipsel.changes C1629605
+Finished at 20151221-1337
+Build needed 00:14:37, 19908k disc space
+Signature with key '5E8F15CF' requested:
+ signfile /home/buildd/build/samtools_1.2-4_mipsel.changes 5E8F15CF
Successfully signed changes file
diff --git a/ppc64el.log b/ppc64el.log
index e024443..5496f9a 100644
--- a/ppc64el.log
+++ b/ppc64el.log
@@ -2,45 +2,46 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on ppc64el-osuosl-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (ppc64el) 22 Sep 2015 16:10 ║
+║ samtools 1.2-4 (ppc64el) 21 Dec 2015 14:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: ppc64el
Host Architecture: ppc64el
Build Architecture: ppc64el
-I: NOTICE: Log filtering will replace 'build/samtools-WcsdPk/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-WcsdPk' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-4b9bc1a9-86e5-4c4f-bcc5-94dabfd7ad61' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-3bRpPJ/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-3bRpPJ' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-ab2c3439-7a90-4fba-9207-868f8c7627e8' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://debian.osuosl.org unstable InRelease [253 kB]
-Get:2 http://debian.osuosl.org unstable/main Sources [8093 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:4 http://ftp.debian.org unstable InRelease [253 kB]
-Get:5 http://debian.osuosl.org unstable/contrib Sources [59.7 kB]
-Get:6 http://debian.osuosl.org unstable/non-free Sources [106 kB]
-Get:7 http://debian.osuosl.org unstable/main ppc64el Packages [7286 kB]
-Get:8 http://incoming.debian.org buildd-unstable/main Sources [341 kB]
-Get:9 http://debian.osuosl.org unstable/contrib ppc64el Packages [42.7 kB]
-Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
-Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
-Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
-Get:13 http://incoming.debian.org buildd-unstable/main ppc64el Packages [97.8 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib ppc64el Packages [1060 B]
-Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
-Get:17 http://ftp.debian.org unstable/main ppc64el Packages [7286 kB]
-Get:18 http://ftp.debian.org unstable/contrib ppc64el Packages [42.7 kB]
-Fetched 32.2 MB in 7s (4218 kB/s)
+Get:1 http://debian.osuosl.org/debian unstable InRelease [265 kB]
+Get:2 http://debian.osuosl.org/debian unstable/main Sources [8421 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:4 http://debian.osuosl.org/debian unstable/contrib Sources [61.8 kB]
+Get:5 http://debian.osuosl.org/debian unstable/non-free Sources [105 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:7 http://debian.osuosl.org/debian unstable/main ppc64el Packages [7702 kB]
+Get:8 http://debian.osuosl.org/debian unstable/contrib ppc64el Packages [45.4 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [199 kB]
+Get:10 http://ftp.debian.org/debian unstable/main Sources [8421 kB]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [32 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1388 B]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/main ppc64el Packages [177 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib ppc64el Packages [568 B]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [61.8 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [105 kB]
+Get:17 http://ftp.debian.org/debian unstable/main ppc64el Packages [7702 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib ppc64el Packages [45.4 kB]
+Fetched 33.7 MB in 9s (3572 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,11 +61,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 2s (1872 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 3s (1151 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,12 +82,18 @@ 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-NwlZLO/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-BtwcEv/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]
+Get:1 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ Packages [529 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -96,23 +106,31 @@ Building dependency tree...
Reading state information...
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 8 not upgraded.
-Need to get 0 B/772 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
+Need to get 0 B/770 B of archives.
After this operation, 0 B of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-BtwcEv/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+debconf: delaying package configuration, since apt-utils is not installed
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 ... 11740 files and directories currently installed.)
+(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 ... 12151 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) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-HBCtap/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-mIjJWx/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]
+Get:1 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ Packages [734 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -123,97 +141,105 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 8 not upgraded.
-Need to get 17.9 MB/17.9 MB of archives.
-After this operation, 69.6 MB of additional disk space will be used.
-Get:1 http://debian.osuosl.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://debian.osuosl.org/debian/ unstable/main groff-base ppc64el 1.22.3-1 [1237 kB]
-Get:3 http://debian.osuosl.org/debian/ unstable/main bsdmainutils ppc64el 9.0.6 [181 kB]
-Get:4 http://debian.osuosl.org/debian/ unstable/main libpipeline1 ppc64el 1.4.1-1 [26.4 kB]
-Get:5 http://debian.osuosl.org/debian/ unstable/main man-db ppc64el 2.7.3-1 [984 kB]
-Get:6 http://debian.osuosl.org/debian/ unstable/main libffi6 ppc64el 3.2.1-3 [20.4 kB]
-Get:7 http://debian.osuosl.org/debian/ unstable/main libglib2.0-0 ppc64el 2.44.1-1.1 [2334 kB]
-Get:8 http://debian.osuosl.org/debian/ unstable/main libicu55 ppc64el 55.1-5 [7624 kB]
-Get:9 http://debian.osuosl.org/debian/ unstable/main libxml2 ppc64el 2.9.2+zdfsg1-4 [827 kB]
-Get:10 http://debian.osuosl.org/debian/ unstable/main libcroco3 ppc64el 0.6.8-3+b1 [125 kB]
-Get:11 http://debian.osuosl.org/debian/ unstable/main libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
-Get:12 http://debian.osuosl.org/debian/ unstable/main libmagic1 ppc64el 1:5.25-1 [253 kB]
-Get:13 http://debian.osuosl.org/debian/ unstable/main file ppc64el 1:5.25-1 [61.6 kB]
-Get:14 http://debian.osuosl.org/debian/ unstable/main gettext-base ppc64el 0.19.6-1 [121 kB]
-Get:15 http://debian.osuosl.org/debian/ unstable/main gettext ppc64el 0.19.6-1 [1418 kB]
-Get:16 http://debian.osuosl.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://debian.osuosl.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://debian.osuosl.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://debian.osuosl.org/debian/ unstable/main libhts1 ppc64el 1.2.1-1 [216 kB]
-Get:20 http://debian.osuosl.org/debian/ unstable/main libhts-dev ppc64el 1.2.1-1 [274 kB]
-Get:21 http://debian.osuosl.org/debian/ unstable/main libio-pty-perl ppc64el 1:1.08-1 [35.0 kB]
-Get:22 http://debian.osuosl.org/debian/ unstable/main libtinfo-dev ppc64el 6.0+20150810-1 [77.8 kB]
-Get:23 http://debian.osuosl.org/debian/ unstable/main libncurses5-dev ppc64el 6.0+20150810-1 [172 kB]
-Get:24 http://debian.osuosl.org/debian/ unstable/main tabix ppc64el 1.2.1-1 [206 kB]
-Get:25 http://debian.osuosl.org/debian/ unstable/main zlib1g-dev ppc64el 1:1.2.8.dfsg-2+b1 [206 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 5 not upgraded.
+Need to get 18.3 MB/18.3 MB of archives.
+After this operation, 71.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-mIjJWx/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [978 B]
+Get:2 http://debian.osuosl.org/debian unstable/main ppc64el bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://debian.osuosl.org/debian unstable/main ppc64el groff-base ppc64el 1.22.3-4 [1239 kB]
+Get:4 http://debian.osuosl.org/debian unstable/main ppc64el bsdmainutils ppc64el 9.0.6+b1 [181 kB]
+Get:5 http://debian.osuosl.org/debian unstable/main ppc64el libpipeline1 ppc64el 1.4.1-1 [26.4 kB]
+Get:6 http://debian.osuosl.org/debian unstable/main ppc64el man-db ppc64el 2.7.5-1 [985 kB]
+Get:7 http://debian.osuosl.org/debian unstable/main ppc64el libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
+Get:8 http://debian.osuosl.org/debian unstable/main ppc64el libmagic1 ppc64el 1:5.25-2 [253 kB]
+Get:9 http://debian.osuosl.org/debian unstable/main ppc64el file ppc64el 1:5.25-2 [61.7 kB]
+Get:10 http://debian.osuosl.org/debian unstable/main ppc64el gettext-base ppc64el 0.19.6-1 [121 kB]
+Get:11 http://debian.osuosl.org/debian unstable/main ppc64el libicu55 ppc64el 55.1-6 [7630 kB]
+Get:12 http://debian.osuosl.org/debian unstable/main ppc64el libxml2 ppc64el 2.9.3+dfsg1-1 [830 kB]
+Get:13 http://debian.osuosl.org/debian unstable/main ppc64el libffi6 ppc64el 3.2.1-4 [20.5 kB]
+Get:14 http://debian.osuosl.org/debian unstable/main ppc64el libglib2.0-0 ppc64el 2.46.2-1 [2503 kB]
+Get:15 http://debian.osuosl.org/debian unstable/main ppc64el libcroco3 ppc64el 0.6.11-1 [133 kB]
+Get:16 http://debian.osuosl.org/debian unstable/main ppc64el gettext ppc64el 0.19.6-1 [1418 kB]
+Get:17 http://debian.osuosl.org/debian unstable/main ppc64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://debian.osuosl.org/debian unstable/main ppc64el po-debconf all 1.0.18 [248 kB]
+Get:19 http://debian.osuosl.org/debian unstable/main ppc64el libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://debian.osuosl.org/debian unstable/main ppc64el libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://debian.osuosl.org/debian unstable/main ppc64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://debian.osuosl.org/debian unstable/main ppc64el dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://debian.osuosl.org/debian unstable/main ppc64el debhelper all 9.20151220 [830 kB]
+Get:24 http://debian.osuosl.org/debian unstable/main ppc64el libhts1 ppc64el 1.2.1-2 [212 kB]
+Get:25 http://debian.osuosl.org/debian unstable/main ppc64el libhts-dev ppc64el 1.2.1-2 [272 kB]
+Get:26 http://debian.osuosl.org/debian unstable/main ppc64el libio-pty-perl ppc64el 1:1.08-1.1+b1 [33.0 kB]
+Get:27 http://debian.osuosl.org/debian unstable/main ppc64el libtinfo-dev ppc64el 6.0+20151024-2 [77.6 kB]
+Get:28 http://debian.osuosl.org/debian unstable/main ppc64el libncurses5-dev ppc64el 6.0+20151024-2 [175 kB]
+Get:29 http://debian.osuosl.org/debian unstable/main ppc64el tabix ppc64el 1.2.1-2 [202 kB]
+Get:30 http://debian.osuosl.org/debian unstable/main ppc64el zlib1g-dev ppc64el 1:1.2.8.dfsg-2+b1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 17.9 MB in 0s (26.1 MB/s)
+Fetched 18.3 MB in 0s (20.6 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11740 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(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 ... 12151 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_ppc64el.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_ppc64el.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_ppc64el.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_ppc64el.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:ppc64el.
Preparing to unpack .../libpipeline1_1.4.1-1_ppc64el.deb ...
Unpacking libpipeline1:ppc64el (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_ppc64el.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:ppc64el.
-Preparing to unpack .../libffi6_3.2.1-3_ppc64el.deb ...
-Unpacking libffi6:ppc64el (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:ppc64el.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_ppc64el.deb ...
-Unpacking libglib2.0-0:ppc64el (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:ppc64el.
-Preparing to unpack .../libicu55_55.1-5_ppc64el.deb ...
-Unpacking libicu55:ppc64el (55.1-5) ...
-Selecting previously unselected package libxml2:ppc64el.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_ppc64el.deb ...
-Unpacking libxml2:ppc64el (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libcroco3:ppc64el.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_ppc64el.deb ...
-Unpacking libcroco3:ppc64el (0.6.8-3+b1) ...
+Preparing to unpack .../man-db_2.7.5-1_ppc64el.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:ppc64el.
Preparing to unpack .../libunistring0_0.9.3-5.2+b1_ppc64el.deb ...
Unpacking libunistring0:ppc64el (0.9.3-5.2+b1) ...
Selecting previously unselected package libmagic1:ppc64el.
-Preparing to unpack .../libmagic1_1%3a5.25-1_ppc64el.deb ...
-Unpacking libmagic1:ppc64el (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_ppc64el.deb ...
+Unpacking libmagic1:ppc64el (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_ppc64el.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_ppc64el.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_ppc64el.deb ...
Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:ppc64el.
+Preparing to unpack .../libicu55_55.1-6_ppc64el.deb ...
+Unpacking libicu55:ppc64el (55.1-6) ...
+Selecting previously unselected package libxml2:ppc64el.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_ppc64el.deb ...
+Unpacking libxml2:ppc64el (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:ppc64el.
+Preparing to unpack .../libffi6_3.2.1-4_ppc64el.deb ...
+Unpacking libffi6:ppc64el (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:ppc64el.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_ppc64el.deb ...
+Unpacking libglib2.0-0:ppc64el (2.46.2-1) ...
+Selecting previously unselected package libcroco3:ppc64el.
+Preparing to unpack .../libcroco3_0.6.11-1_ppc64el.deb ...
+Unpacking libcroco3:ppc64el (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_ppc64el.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -223,72 +249,90 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:ppc64el.
-Preparing to unpack .../libhts1_1.2.1-1_ppc64el.deb ...
-Unpacking libhts1:ppc64el (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_ppc64el.deb ...
+Unpacking libhts1:ppc64el (1.2.1-2) ...
Selecting previously unselected package libhts-dev:ppc64el.
-Preparing to unpack .../libhts-dev_1.2.1-1_ppc64el.deb ...
-Unpacking libhts-dev:ppc64el (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_ppc64el.deb ...
+Unpacking libhts-dev:ppc64el (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1_ppc64el.deb ...
-Unpacking libio-pty-perl (1:1.08-1) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_ppc64el.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:ppc64el.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_ppc64el.deb ...
-Unpacking libtinfo-dev:ppc64el (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_ppc64el.deb ...
+Unpacking libtinfo-dev:ppc64el (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:ppc64el.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_ppc64el.deb ...
-Unpacking libncurses5-dev:ppc64el (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_ppc64el.deb ...
+Unpacking libncurses5-dev:ppc64el (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_ppc64el.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../tabix_1.2.1-2_ppc64el.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:ppc64el.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_ppc64el.deb ...
Unpacking zlib1g-dev:ppc64el (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:ppc64el (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:ppc64el (3.2.1-3) ...
-Setting up libglib2.0-0:ppc64el (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:ppc64el (55.1-5) ...
-Setting up libxml2:ppc64el (2.9.2+zdfsg1-4) ...
-Setting up libcroco3:ppc64el (0.6.8-3+b1) ...
Setting up libunistring0:ppc64el (0.9.3-5.2+b1) ...
-Setting up libmagic1:ppc64el (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:ppc64el (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:ppc64el (55.1-6) ...
+Setting up libxml2:ppc64el (2.9.3+dfsg1-1) ...
+Setting up libffi6:ppc64el (3.2.1-4) ...
+Setting up libglib2.0-0:ppc64el (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:ppc64el (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:ppc64el (1.2.1-1) ...
-Setting up libhts-dev:ppc64el (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1) ...
-Setting up libtinfo-dev:ppc64el (6.0+20150810-1) ...
-Setting up libncurses5-dev:ppc64el (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:ppc64el (1.2.1-2) ...
+Setting up libhts-dev:ppc64el (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:ppc64el (6.0+20151024-2) ...
+Setting up libncurses5-dev:ppc64el (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-powerpc64le ppc64el (ppc64le)
-Toolchain package versions: binutils_2.25.1-1 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_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 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+b2 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b2 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4+b2 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -299,15 +343,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -326,17 +371,19 @@ SCHROOT_CHROOT_NAME=sid-ppc64el-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ppc64el-sbuild-4b9bc1a9-86e5-4c4f-bcc5-94dabfd7ad61
+SCHROOT_SESSION_ID=sid-ppc64el-sbuild-ab2c3439-7a90-4fba-9207-868f8c7627e8
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture ppc64el
@@ -474,82 +521,82 @@ dh_auto_test -- \
make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-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/V45HaBNwUA/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/oWFXottKCB/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/V45HaBNwUA/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/oWFXottKCB/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/V45HaBNwUA/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/oWFXottKCB/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/V45HaBNwUA/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/oWFXottKCB/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/V45HaBNwUA/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/oWFXottKCB/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/V45HaBNwUA/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/oWFXottKCB/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/V45HaBNwUA/mpileup.bam.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/oWFXottKCB/mpileup.bam.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/V45HaBNwUA/mpileup.bam.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/oWFXottKCB/mpileup.bam.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/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/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/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/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/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/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/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/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/V45HaBNwUA/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oWFXottKCB/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/V45HaBNwUA/mpileup.1.cram | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oWFXottKCB/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -779,80 +826,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/V45HaBNwUA/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/oWFXottKCB/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/V45HaBNwUA/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/oWFXottKCB/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/V45HaBNwUA/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/oWFXottKCB/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/V45HaBNwUA/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/oWFXottKCB/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/oWFXottKCB/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/oWFXottKCB/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/oWFXottKCB/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/V45HaBNwUA/view.test067.sam -h -l Library 2 /tmp/V45HaBNwUA/view.001.sam
+ 67: Filter -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/oWFXottKCB/view.test067.sam -h -l Library 2 /tmp/oWFXottKCB/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/V45HaBNwUA/view.001.sam
+ 68: Count -l Library 2 (SAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/oWFXottKCB/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/V45HaBNwUA/view.test069.sam -h -l Library 2 /tmp/V45HaBNwUA/view.test001.bam
+ 69: Filter -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/oWFXottKCB/view.test069.sam -h -l Library 2 /tmp/oWFXottKCB/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/V45HaBNwUA/view.test001.bam
+ 70: Count -l Library 2 (BAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/oWFXottKCB/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/V45HaBNwUA/view.test071.sam -h -l Library 2 /tmp/V45HaBNwUA/view.test006.cram
+ 71: Filter -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/oWFXottKCB/view.test071.sam -h -l Library 2 /tmp/oWFXottKCB/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/V45HaBNwUA/view.test006.cram
+ 72: Count -l Library 2 (CRAM input) Samtools-htslib-API: bam_get_library() not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/oWFXottKCB/view.test006.cram
.. expected failure
@@ -1299,82 +1346,82 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
-Unsorted mode enabled
- Generate CRAM file .. ok
+ Generate CRAM file Unsorted mode enabled
+.. ok
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
+ 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
+ 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
+ 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
+ 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
+ 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
+ 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+.. ok
test_depad:
Generate BAM file .. ok
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
+ depad (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
+ depad -s (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
+ depad -u (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
+ depad -1 (SAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
/«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
.. expected failure
-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/V45HaBNwUA/depad.001p.bam
+ depad (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/oWFXottKCB/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/V45HaBNwUA/depad.001p.bam
+ depad -s (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/oWFXottKCB/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/V45HaBNwUA/depad.001p.bam
+ depad -u (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/oWFXottKCB/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/V45HaBNwUA/depad.001p.bam
+ depad -1 (BAM input) Samtools-htslib: fix_header() header parsing not yet implemented
+ Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/oWFXottKCB/depad.001p.bam
.. expected failure
@@ -1412,7 +1459,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/FMbWO6d3XC - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/jBiMx9gPPd - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1506,6 +1553,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -1518,17 +1568,30 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -1536,31 +1599,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/powerpc64le-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/lib/powerpc64le-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/01
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/01/2298564ec26406fab3dcc1b73c32566aab9dd5.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/01/2298564ec26406fab3dcc1b73c32566aab9dd5.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/01/2298564ec26406fab3dcc1b73c32566aab9dd5.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cd
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cd/0a88dddd6d4f33892eeb7d41431989d14e439f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cd/0a88dddd6d4f33892eeb7d41431989d14e439f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cd/0a88dddd6d4f33892eeb7d41431989d14e439f.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/05
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/05/68e92a96bc3886ad0cb77697b0f55ddc5ae637.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/05/68e92a96bc3886ad0cb77697b0f55ddc5ae637.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/05/68e92a96bc3886ad0cb77697b0f55ddc5ae637.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fc
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fc/5b43fb114a88db68e41b7a755f9d5070643e6c.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fc/5b43fb114a88db68e41b7a755f9d5070643e6c.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fc/5b43fb114a88db68e41b7a755f9d5070643e6c.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3b
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3b/0e6e79fa97b4ea4cd1ac5af801628e55f719be.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3b/0e6e79fa97b4ea4cd1ac5af801628e55f719be.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/3b/0e6e79fa97b4ea4cd1ac5af801628e55f719be.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/50
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/50/23f0cfb9b1ea92b98358bddea515a93104861c.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/50/23f0cfb9b1ea92b98358bddea515a93104861c.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/50/23f0cfb9b1ea92b98358bddea515a93104861c.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/45
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/45/1a6557c9fb831c40eb38c31f3ead001e96622f.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/45/1a6557c9fb831c40eb38c31f3ead001e96622f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/45/1a6557c9fb831c40eb38c31f3ead001e96622f.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=012298564ec26406fab3dcc1b73c32566aab9dd5 0568e92a96bc3886ad0cb77697b0f55ddc5ae637 3b0e6e79fa97b4ea4cd1ac5af801628e55 [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -1570,16 +1669,22 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_ppc64el.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_ppc64el.deb'.
- dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org> >../samtools_1.2-3_ppc64el.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_ppc64el.deb'.
+ dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org> >../samtools_1.2-4_ppc64el.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1614
+Build finished at 20151221-1444
Finished
────────
@@ -1596,54 +1701,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_ppc64el.changes:
+samtools_1.2-4_ppc64el.changes:
───────────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: ppc64el
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
Maintainer: ppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- 7baa0c425137bb89ec61606ee03386e7ad27fd62 376902 samtools_1.2-3_ppc64el.deb
+ 30062220dbde816902edc104dfb4685a985475c8 415906 samtools-dbgsym_1.2-4_ppc64el.deb
+ 39cbe3f009bc5fdd01fe895258ba362919b6d235 372672 samtools_1.2-4_ppc64el.deb
Checksums-Sha256:
- f6d8ae5f0f5184a7e6f313141e5b17be430381e876aa5a1f04c2b4819fb86ff3 376902 samtools_1.2-3_ppc64el.deb
+ 1394f1ff345a2b5d8832fd4ce9b132b858e346c2ed608542a4b0ca8785bb272a 415906 samtools-dbgsym_1.2-4_ppc64el.deb
+ 251b43d66f98d66241da018f3bef1a1b5f09e28f4382b27e979a26f757269590 372672 samtools_1.2-4_ppc64el.deb
Files:
- 7ea932e83a5844dc64981b8a7ab520ef 376902 science optional samtools_1.2-3_ppc64el.deb
+ bf292737b8481732b27cff9c70ed27c5 415906 debug extra samtools-dbgsym_1.2-4_ppc64el.deb
+ 84f447214c80dec433960d465c3e562f 372672 science optional samtools_1.2-4_ppc64el.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_ppc64el.deb
+samtools-dbgsym_1.2-4_ppc64el.deb
+─────────────────────────────────
+
+ new debian package, version 2.0.
+ size 415906 bytes: control archive=817 bytes.
+ 648 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: ppc64el
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 514
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 012298564ec26406fab3dcc1b73c32566aab9dd5 0568e92a96bc3886ad0cb77697b0f55ddc5ae637 3b0e6e79fa97b4ea4cd1ac5af801628e55f719be 451a6557c9fb831c40eb38c31f3ead001e96622f 5023f0cfb9b1ea92b98358bddea515a93104861c cd0a88dddd6d4f33892eeb7d41431989d14e439f fc5b43fb114a88db68e41b7a755f9d5070643e6c
+
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/01/
+-rw-r--r-- root/root 21120 2015-12-21 14:44 ./usr/lib/debug/.build-id/01/2298564ec26406fab3dcc1b73c32566aab9dd5.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/05/
+-rw-r--r-- root/root 15072 2015-12-21 14:44 ./usr/lib/debug/.build-id/05/68e92a96bc3886ad0cb77697b0f55ddc5ae637.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/3b/
+-rw-r--r-- root/root 13048 2015-12-21 14:44 ./usr/lib/debug/.build-id/3b/0e6e79fa97b4ea4cd1ac5af801628e55f719be.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/45/
+-rw-r--r-- root/root 412296 2015-12-21 14:44 ./usr/lib/debug/.build-id/45/1a6557c9fb831c40eb38c31f3ead001e96622f.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/50/
+-rw-r--r-- root/root 21464 2015-12-21 14:44 ./usr/lib/debug/.build-id/50/23f0cfb9b1ea92b98358bddea515a93104861c.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/cd/
+-rw-r--r-- root/root 11776 2015-12-21 14:44 ./usr/lib/debug/.build-id/cd/0a88dddd6d4f33892eeb7d41431989d14e439f.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/lib/debug/.build-id/fc/
+-rw-r--r-- root/root 13064 2015-12-21 14:44 ./usr/lib/debug/.build-id/fc/5b43fb114a88db68e41b7a755f9d5070643e6c.debug
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 14:44 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_ppc64el.deb
──────────────────────────
new debian package, version 2.0.
- size 376902 bytes: control archive=1489 bytes.
- 805 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 372672 bytes: control archive=1608 bytes.
+ 810 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: ppc64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1485
+ Installed-Size: 1492
Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1653,44 +1811,51 @@ samtools_1.2-3_ppc64el.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 16:14 ./
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/bin/
--rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/ace2sam
+ one 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 2015-12-21 14:44 ./
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/bin/
+-rwxr-xr-x root/root 67696 2015-12-21 14:44 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 67672 2015-09-22 16:14 ./usr/bin/md5fa
--rwxr-xr-x root/root 67672 2015-09-22 16:14 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 67672 2015-12-21 14:44 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 67672 2015-12-21 14:44 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 67664 2015-12-21 14:44 ./usr/bin/md5fa
+-rwxr-xr-x root/root 67608 2015-12-21 14:44 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 920504 2015-09-22 16:14 ./usr/bin/samtools
+-rwxr-xr-x root/root 921128 2015-12-21 14:44 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 67768 2015-09-22 16:14 ./usr/bin/wgsim
+-rwxr-xr-x root/root 67784 2015-12-21 14:44 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 16:14 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 14:44 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 14:44 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 14:44 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 14:44 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 14:44 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1710,23 +1875,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: ppc64el
-Build-Space: 35892
-Build-Time: 199
+Build-Space: 37892
+Build-Time: 196
Distribution: sid
Host Architecture: ppc64el
-Install-Time: 8
-Job: samtools_1.2-3
+Install-Time: 10
+Job: samtools_1.2-4
Machine Architecture: ppc64el
Package: samtools
-Package-Time: 225
-Source-Version: 1.2-3
-Space: 35892
+Package-Time: 230
+Source-Version: 1.2-4
+Space: 37892
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1614
-Build needed 00:03:45, 35892k disc space
+Finished at 20151221-1444
+Build needed 00:03:50, 37892k disc space
Signature with key 'AE6C7FBC' requested:
- signfile /home/buildd/build/samtools_1.2-3_ppc64el.changes AE6C7FBC
+ signfile /home/buildd/build/samtools_1.2-4_ppc64el.changes AE6C7FBC
Successfully signed changes file
diff --git a/x32.log b/sh4.log
similarity index 54%
copy from x32.log
copy to sh4.log
index 9e4d453..0c011ef 100644
--- a/x32.log
+++ b/sh4.log
@@ -1,65 +1,41 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs76.physik.fu-berlin.de
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs95.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (x32) 22 Sep 2015 18:49 ║
+║ samtools 1.2-4 (sh4) 14 Jan 2016 16:38 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: amd64
-Host Architecture: x32
-Build Architecture: x32
+Host Architecture: sh4
+Build Architecture: sh4
-I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-cept5Y/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-cept5Y' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-sh4-sbuild-7486bb18-f913-4a8a-a2f9-e0ce446404e9' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org unstable InRelease [253 kB]
-Get:2 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:3 http://incoming.debian.org buildd-unstable/main Sources [353 kB]
-Get:4 http://ftp.debian.org unstable/main Sources/DiffIndex [7876 B]
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-Ign http://incoming.debian-ports.org unstable InRelease
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-Get:7 http://ftp.debian.org unstable/main 2015-09-17-2033.47.pdiff [17.0 kB]
-Get:8 http://ftp.debian.org unstable/main 2015-09-18-0236.10.pdiff [2554 B]
-Get:9 http://ftp.debian.org unstable/main 2015-09-18-0836.19.pdiff [3115 B]
-Get:10 http://ftp.debian.org unstable/main 2015-09-18-1434.45.pdiff [20.1 kB]
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-Get:14 http://ftp.debian-ports.org unreleased InRelease [44.8 kB]
-Get:15 http://ftp.debian.org unstable/main 2015-09-19-0836.28.pdiff [5086 B]
-Get:16 http://ftp.debian.org unstable/main 2015-09-19-1440.27.pdiff [12.2 kB]
-Get:17 http://ftp.debian.org unstable/main 2015-09-19-2034.22.pdiff [28.8 kB]
-Get:18 http://ftp.debian.org unstable/main 2015-09-20-0235.43.pdiff [10.9 kB]
-Get:19 http://incoming.debian-ports.org unstable Release [39.6 kB]
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-Get:23 http://ftp.debian.org unstable/main 2015-09-21-0236.32.pdiff [8959 B]
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-Get:30 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
-Get:31 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
-Get:32 http://incoming.debian-ports.org unstable/main x32 Packages [36.7 kB]
-Ign http://incoming.debian-ports.org unstable/main Translation-en
-Get:33 http://ftp.debian-ports.org unreleased/main x32 Packages [63.0 kB]
-Ign http://ftp.debian-ports.org unstable/main Translation-en
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Fetched 14.2 MB in 10s (1346 kB/s)
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Ign:2 http://incoming.debian-ports.org/buildd unstable InRelease
+Get:3 ftp://ftp.debian.org/debian unstable InRelease [277 kB]
+Get:4 http://incoming.debian-ports.org/buildd unstable Release [43.8 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable InRelease [37.1 kB]
+Get:6 http://incoming.debian-ports.org/buildd unstable Release.gpg [836 B]
+Get:7 ftp://ftp.debian-ports.org/debian unreleased InRelease [40.8 kB]
+Get:8 ftp://ftp.debian.org/debian unstable/main Sources.diff/Index [27.9 kB]
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+Get:12 ftp://ftp.debian-ports.org/debian unstable/main sh4 Packages [13.6 MB]
+Fetched 22.9 MB in 41s (551 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -79,11 +55,14 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 2s (1775 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 ftp://ftp.debian.org/debian unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 ftp://ftp.debian.org/debian unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 ftp://ftp.debian.org/debian unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 1s (2697 kB/s)
Download complete and in download only mode
Check architectures
@@ -95,13 +74,18 @@ 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-ba45YF/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-SwNrbQ/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
+Get:1 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ Packages [524 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -112,40 +96,47 @@ Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
+The following additional packages will be installed:
fakeroot libfakeroot
The following NEW packages will be installed:
fakeroot libfakeroot sbuild-build-depends-core-dummy
-0 upgraded, 3 newly installed, 0 to remove and 24 not upgraded.
-Need to get 129 kB/130 kB of archives.
-After this operation, 411 kB of additional disk space will be used.
-Get:1 http://ftp.debian-ports.org/debian/ unstable/main libfakeroot x32 1.20.2-1 [44.8 kB]
-Get:2 http://ftp.debian-ports.org/debian/ unstable/main fakeroot x32 1.20.2-1 [84.6 kB]
+0 upgraded, 3 newly installed, 0 to remove and 39 not upgraded.
+Need to get 130 kB/131 kB of archives.
+After this operation, 403 kB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-SwNrbQ/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
+Get:2 ftp://ftp.debian-ports.org/debian unstable/main sh4 libfakeroot sh4 1.20.2-1 [42.0 kB]
+Get:3 ftp://ftp.debian-ports.org/debian unstable/main sh4 fakeroot sh4 1.20.2-1 [88.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 129 kB in 1s (115 kB/s)
-Selecting previously unselected package libfakeroot:x32.
-(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12802 files and directories currently installed.)
-Preparing to unpack .../libfakeroot_1.20.2-1_x32.deb ...
-Unpacking libfakeroot:x32 (1.20.2-1) ...
+Fetched 130 kB in 3s (34.4 kB/s)
+Selecting previously unselected package libfakeroot:sh4.
+(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%
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(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 ... 12094 files and directories currently installed.)
+Preparing to unpack .../libfakeroot_1.20.2-1_sh4.deb ...
+Unpacking libfakeroot:sh4 (1.20.2-1) ...
Selecting previously unselected package fakeroot.
-Preparing to unpack .../fakeroot_1.20.2-1_x32.deb ...
+Preparing to unpack .../fakeroot_1.20.2-1_sh4.deb ...
Unpacking fakeroot (1.20.2-1) ...
Selecting previously unselected package sbuild-build-depends-core-dummy.
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up libfakeroot:x32 (1.20.2-1) ...
+Setting up libfakeroot:sh4 (1.20.2-1) ...
Setting up fakeroot (1.20.2-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
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-7knP0Q/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-LxyaHx/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
+Get:1 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ Packages [732 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -156,172 +147,198 @@ Installing build dependencies
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 24 not upgraded.
-Need to get 18.3 MB/18.3 MB of archives.
-After this operation, 64.0 MB of additional disk space will be used.
-Get:1 http://ftp.debian-ports.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp.debian-ports.org/debian/ unstable/main groff-base x32 1.22.3-1 [1199 kB]
-Get:3 http://ftp.debian-ports.org/debian/ unstable/main bsdmainutils x32 9.0.6 [183 kB]
-Get:4 http://ftp.debian-ports.org/debian/ unstable/main libpipeline1 x32 1.4.1-1 [28.0 kB]
-Get:5 http://ftp.debian-ports.org/debian/ unstable/main man-db x32 2.7.3-1 [1003 kB]
-Get:6 http://ftp.debian-ports.org/debian/ unstable/main libffi6 x32 3.2.1-3 [19.9 kB]
-Get:7 http://ftp.debian-ports.org/debian/ unstable/main libunistring0 x32 0.9.3-5.2 [289 kB]
-Get:8 http://ftp.debian-ports.org/debian/ unstable/main libmagic1 x32 1:5.25-1 [256 kB]
-Get:9 http://ftp.debian-ports.org/debian/ unstable/main file x32 1:5.25-1 [61.5 kB]
-Get:10 http://ftp.debian-ports.org/debian/ unstable/main gettext-base x32 0.19.6-1 [123 kB]
-Get:11 http://ftp.debian-ports.org/debian/ unstable/main libicu55 x32 55.1-5 [7659 kB]
-Get:12 http://ftp.debian-ports.org/debian/ unstable/main libxml2 x32 2.9.2+zdfsg1-4 [924 kB]
-Get:13 http://ftp.debian-ports.org/debian/ unstable/main libglib2.0-0 x32 2.44.1-1.1 [2471 kB]
-Get:14 http://ftp.debian-ports.org/debian/ unstable/main libcroco3 x32 0.6.8-3+b1 [135 kB]
-Get:15 http://ftp.debian-ports.org/debian/ unstable/main gettext x32 0.19.6-1 [1466 kB]
-Get:16 http://ftp.debian-ports.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.debian-ports.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.debian-ports.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.debian-ports.org/debian/ unstable/main libhts1 x32 1.2.1-1 [226 kB]
-Get:20 http://ftp.debian-ports.org/debian/ unstable/main libhts-dev x32 1.2.1-1 [274 kB]
-Get:21 http://ftp.debian-ports.org/debian/ unstable/main libio-pty-perl x32 1:1.08-1+b2 [36.0 kB]
-Get:22 http://ftp.debian-ports.org/debian/ unstable/main libtinfo-dev x32 6.0+20150810-1 [76.5 kB]
-Get:23 http://ftp.debian-ports.org/debian/ unstable/main libncurses5-dev x32 6.0+20150810-1 [170 kB]
-Get:24 http://ftp.debian-ports.org/debian/ unstable/main tabix x32 1.2.1-1 [221 kB]
-Get:25 http://ftp.debian-ports.org/debian/ unstable/main zlib1g-dev x32 1:1.2.8.dfsg-2+b1 [206 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 39 not upgraded.
+Need to get 18.8 MB/18.8 MB of archives.
+After this operation, 62.9 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-LxyaHx/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [974 B]
+Get:2 ftp://ftp.debian-ports.org/debian unstable/main sh4 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 ftp://ftp.debian-ports.org/debian unstable/main sh4 groff-base sh4 1.22.3-5 [1248 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main sh4 bsdmainutils sh4 9.0.6+b1 [184 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable/main sh4 libpipeline1 sh4 1.4.1-2 [30.8 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unstable/main sh4 man-db sh4 2.7.5-1 [1007 kB]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main sh4 libunistring0 sh4 0.9.3-5.2 [283 kB]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main sh4 libmagic1 sh4 1:5.25-2 [264 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main sh4 file sh4 1:5.25-2 [61.5 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main sh4 gettext-base sh4 0.19.6-1 [123 kB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main sh4 libicu55 sh4 55.1-7 [7775 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main sh4 libxml2 sh4 2.9.3+dfsg1-1 [940 kB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main sh4 libffi6 sh4 3.2.1-4 [20.4 kB]
+Get:14 ftp://ftp.debian-ports.org/debian unstable/main sh4 libglib2.0-0 sh4 2.46.2-3 [2624 kB]
+Get:15 ftp://ftp.debian-ports.org/debian unstable/main sh4 libcroco3 sh4 0.6.11-1 [141 kB]
+Get:16 ftp://ftp.debian-ports.org/debian unstable/main sh4 gettext sh4 0.19.6-1 [1476 kB]
+Get:17 ftp://ftp.debian-ports.org/debian unstable/main sh4 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 ftp://ftp.debian-ports.org/debian unstable/main sh4 po-debconf all 1.0.19 [249 kB]
+Get:19 ftp://ftp.debian-ports.org/debian unstable/main sh4 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:20 ftp://ftp.debian-ports.org/debian unstable/main sh4 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main sh4 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 ftp://ftp.debian-ports.org/debian unstable/main sh4 debhelper all 9.20151225 [830 kB]
+Get:24 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts1 sh4 1.2.1-2 [245 kB]
+Get:25 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts-dev sh4 1.2.1-2 [279 kB]
+Get:26 ftp://ftp.debian-ports.org/debian unstable/main sh4 libio-pty-perl sh4 1:1.08-1.1 [34.6 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtinfo-dev sh4 6.0+20151024-2 [73.2 kB]
+Get:28 ftp://ftp.debian-ports.org/debian unstable/main sh4 libncurses5-dev sh4 6.0+20151024-2 [165 kB]
+Get:29 ftp://ftp.debian-ports.org/debian unstable/main sh4 tabix sh4 1.2.1-2 [213 kB]
+Get:30 ftp://ftp.debian-ports.org/debian unstable/main sh4 zlib1g-dev sh4 1:1.2.8.dfsg-2+b1 [202 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.3 MB in 10s (1822 kB/s)
+Fetched 18.8 MB in 49s (380 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12852 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12143 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_x32.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-5_sh4.deb ...
+Unpacking groff-base (1.22.3-5) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_x32.deb ...
-Unpacking bsdmainutils (9.0.6) ...
-Selecting previously unselected package libpipeline1:x32.
-Preparing to unpack .../libpipeline1_1.4.1-1_x32.deb ...
-Unpacking libpipeline1:x32 (1.4.1-1) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_sh4.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
+Selecting previously unselected package libpipeline1:sh4.
+Preparing to unpack .../libpipeline1_1.4.1-2_sh4.deb ...
+Unpacking libpipeline1:sh4 (1.4.1-2) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_x32.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:x32.
-Preparing to unpack .../libffi6_3.2.1-3_x32.deb ...
-Unpacking libffi6:x32 (3.2.1-3) ...
-Selecting previously unselected package libunistring0:x32.
-Preparing to unpack .../libunistring0_0.9.3-5.2_x32.deb ...
-Unpacking libunistring0:x32 (0.9.3-5.2) ...
-Selecting previously unselected package libmagic1:x32.
-Preparing to unpack .../libmagic1_1%3a5.25-1_x32.deb ...
-Unpacking libmagic1:x32 (1:5.25-1) ...
+Preparing to unpack .../man-db_2.7.5-1_sh4.deb ...
+Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package libunistring0:sh4.
+Preparing to unpack .../libunistring0_0.9.3-5.2_sh4.deb ...
+Unpacking libunistring0:sh4 (0.9.3-5.2) ...
+Selecting previously unselected package libmagic1:sh4.
+Preparing to unpack .../libmagic1_1%3a5.25-2_sh4.deb ...
+Unpacking libmagic1:sh4 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_x32.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_sh4.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.6-1_x32.deb ...
+Preparing to unpack .../gettext-base_0.19.6-1_sh4.deb ...
Unpacking gettext-base (0.19.6-1) ...
-Selecting previously unselected package libicu55:x32.
-Preparing to unpack .../libicu55_55.1-5_x32.deb ...
-Unpacking libicu55:x32 (55.1-5) ...
-Selecting previously unselected package libxml2:x32.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_x32.deb ...
-Unpacking libxml2:x32 (2.9.2+zdfsg1-4) ...
-Selecting previously unselected package libglib2.0-0:x32.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_x32.deb ...
-Unpacking libglib2.0-0:x32 (2.44.1-1.1) ...
-Selecting previously unselected package libcroco3:x32.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_x32.deb ...
-Unpacking libcroco3:x32 (0.6.8-3+b1) ...
+Selecting previously unselected package libicu55:sh4.
+Preparing to unpack .../libicu55_55.1-7_sh4.deb ...
+Unpacking libicu55:sh4 (55.1-7) ...
+Selecting previously unselected package libxml2:sh4.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_sh4.deb ...
+Unpacking libxml2:sh4 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:sh4.
+Preparing to unpack .../libffi6_3.2.1-4_sh4.deb ...
+Unpacking libffi6:sh4 (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:sh4.
+Preparing to unpack .../libglib2.0-0_2.46.2-3_sh4.deb ...
+Unpacking libglib2.0-0:sh4 (2.46.2-3) ...
+Selecting previously unselected package libcroco3:sh4.
+Preparing to unpack .../libcroco3_0.6.11-1_sh4.deb ...
+Unpacking libcroco3:sh4 (0.6.11-1) ...
Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.6-1_x32.deb ...
+Preparing to unpack .../gettext_0.19.6-1_sh4.deb ...
Unpacking gettext (0.19.6-1) ...
Selecting previously unselected package intltool-debian.
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) ...
+Preparing to unpack .../po-debconf_1.0.19_all.deb ...
+Unpacking po-debconf (1.0.19) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.56-2_all.deb ...
+Unpacking libarchive-zip-perl (1.56-2) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
-Selecting previously unselected package libhts1:x32.
-Preparing to unpack .../libhts1_1.2.1-1_x32.deb ...
-Unpacking libhts1:x32 (1.2.1-1) ...
-Selecting previously unselected package libhts-dev:x32.
-Preparing to unpack .../libhts-dev_1.2.1-1_x32.deb ...
-Unpacking libhts-dev:x32 (1.2.1-1) ...
+Preparing to unpack .../debhelper_9.20151225_all.deb ...
+Unpacking debhelper (9.20151225) ...
+Selecting previously unselected package libhts1:sh4.
+Preparing to unpack .../libhts1_1.2.1-2_sh4.deb ...
+Unpacking libhts1:sh4 (1.2.1-2) ...
+Selecting previously unselected package libhts-dev:sh4.
+Preparing to unpack .../libhts-dev_1.2.1-2_sh4.deb ...
+Unpacking libhts-dev:sh4 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b2_x32.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b2) ...
-Selecting previously unselected package libtinfo-dev:x32.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_x32.deb ...
-Unpacking libtinfo-dev:x32 (6.0+20150810-1) ...
-Selecting previously unselected package libncurses5-dev:x32.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_x32.deb ...
-Unpacking libncurses5-dev:x32 (6.0+20150810-1) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1_sh4.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1) ...
+Selecting previously unselected package libtinfo-dev:sh4.
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_sh4.deb ...
+Unpacking libtinfo-dev:sh4 (6.0+20151024-2) ...
+Selecting previously unselected package libncurses5-dev:sh4.
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_sh4.deb ...
+Unpacking libncurses5-dev:sh4 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.2.1-1_x32.deb ...
-Unpacking tabix (1.2.1-1) ...
-Selecting previously unselected package zlib1g-dev:x32.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_x32.deb ...
-Unpacking zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Preparing to unpack .../archives/tabix_1.2.1-2_sh4.deb ...
+Unpacking tabix (1.2.1-2) ...
+Selecting previously unselected package zlib1g-dev:sh4.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_sh4.deb ...
+Unpacking zlib1g-dev:sh4 (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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-5) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:x32 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up libpipeline1:sh4 (1.4.1-2) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:x32 (3.2.1-3) ...
-Setting up libunistring0:x32 (0.9.3-5.2) ...
-Setting up libmagic1:x32 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libunistring0:sh4 (0.9.3-5.2) ...
+Setting up libmagic1:sh4 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
-Setting up libicu55:x32 (55.1-5) ...
-Setting up libxml2:x32 (2.9.2+zdfsg1-4) ...
-Setting up libglib2.0-0:x32 (2.44.1-1.1) ...
+Setting up libicu55:sh4 (55.1-7) ...
+Setting up libxml2:sh4 (2.9.3+dfsg1-1) ...
+Setting up libffi6:sh4 (3.2.1-4) ...
+Setting up libglib2.0-0:sh4 (2.46.2-3) ...
No schema files found: doing nothing.
-Setting up libcroco3:x32 (0.6.8-3+b1) ...
+Setting up libcroco3:sh4 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:x32 (1.2.1-1) ...
-Setting up libhts-dev:x32 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b2) ...
-Setting up libtinfo-dev:x32 (6.0+20150810-1) ...
-Setting up libncurses5-dev:x32 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
-Setting up zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:sh4 (1.2.1-2) ...
+Setting up libhts-dev:sh4 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1) ...
+Setting up libtinfo-dev:sh4 (6.0+20151024-2) ...
+Setting up libncurses5-dev:sh4 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
+Setting up zlib1g-dev:sh4 (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20151225) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-17 gcc-4.9_4.9.3-4 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-4.9-dev_4.9.3-4 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_2.25.1-1 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-4.9_4.9.3-4 cpp-5_5.2.1-17 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42. [...]
+Kernel: Linux 4.2.0-0.bpo.1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.4 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8+b1 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151225 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.114-1 dpkg_1.18.3 dpkg-dev_1.18.4 e [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -332,15 +349,16 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
@@ -352,31 +370,28 @@ User Environment
DEB_BUILD_OPTIONS=nobench nocheck
HOME=/sbuild-nonexistent
-LD_LIBRARY_PATH=/usr/lib/libeatmydata
-LD_PRELOAD=libeatmydata.so
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-PWD=/«PKGBUILDDIR»
-SCHROOT_ALIAS_NAME=sid-x32-sbuild
-SCHROOT_CHROOT_NAME=sid-x32-sbuild
+SCHROOT_ALIAS_NAME=sid-sh4-sbuild
+SCHROOT_CHROOT_NAME=sid-sh4-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7
+SCHROOT_SESSION_ID=sid-sh4-sbuild-7486bb18-f913-4a8a-a2f9-e0ce446404e9
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c20511
+XDG_SESSION_ID=c18
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
-dpkg-buildpackage: host architecture x32
+dpkg-buildpackage: host architecture sh4
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
@@ -417,96 +432,96 @@ dh build-arch --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a \
+ HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
-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_index.o bam_index.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_plcmd.o bam_plcmd.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 sam_view.o sam_view.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_cat.o bam_cat.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_md.o bam_md.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_reheader.o bam_reheader.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_sort.o bam_sort.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 bedidx.o bedidx.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 kprobaln.o kprobaln.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_rmdup.o bam_rmdup.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_rmdupse.o bam_rmdupse.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_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
+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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
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 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
-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 sample.o sample.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 cut_target.o cut_target.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 phase.o phase.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 bam2depth.o bam2depth.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 padding.o padding.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 bedcov.o bedcov.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 bamshuf.o bamshuf.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 faidx.o faidx.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 stats.o stats.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 stats_isize.o stats_isize.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_flags.o bam_flags.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_split.o bam_split.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_tview.o bam_tview.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_tview_curses.o bam_tview_curses.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_tview_html.o bam_tview_html.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_lpileup.o bam_lpileup.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_aux.o bam_aux.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.o bam.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_import.o bam_import.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 sam.o sam.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 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
+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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.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 -Wdate-time -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 -Wdate-time -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
-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-gnux32/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
+/usr/bin/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/sh4-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 -Wdate-time -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
+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 -Wdate-time -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.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 -c -o misc/maq2sam-short.o misc/maq2sam.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.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 -c -o misc/md5fa.o misc/md5fa.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 misc/md5.o misc/md5.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.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 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.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 -Wdate-time -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
-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/wgsim.o misc/wgsim.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -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 test/merge/test_bam_translate.o test/merge/test_bam_translate.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 test/test.o test/test.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
-gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
-gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
-gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -c -o test/vcf-miniview.o test/vcf-miniview.c
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-linux-gnux32/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/sh4-linux-gnu/libhts.a -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 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/sh4-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a \
+ HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
@@ -521,9 +536,9 @@ make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
prefix=/usr \
HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a
+ HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a
install -d debian/samtools
- make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a
+ make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a
make[2]: Entering directory '/«PKGBUILDDIR»'
mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
@@ -540,12 +555,42 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -a -O--parallel
install -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
+Unsupported ioctl: cmd=0x40049409
install -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+Unsupported ioctl: cmd=0x40049409
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+Unsupported ioctl: cmd=0x40049409
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+Unsupported ioctl: cmd=0x40049409
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
+Unsupported ioctl: cmd=0x40049409
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+Unsupported ioctl: cmd=0x40049409
cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+Unsupported ioctl: cmd=0x40049409
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
@@ -557,14 +602,27 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -572,13 +630,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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-gnux32/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/lib/sh4-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
@@ -592,7 +650,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
@@ -608,14 +666,14 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/samtools/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_x32.deb'.
- dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.2-3_x32.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_sh4.deb'.
+ dpkg-genchanges -B -mdebian/sh4 buildd <buildd-vs94 at glaubitz.dialup.fu-berlin.de> >../samtools_1.2-4_sh4.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1850
+Build finished at 20160114-1654
Finished
────────
@@ -632,55 +690,60 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_x32.changes:
+samtools_1.2-4_sh4.changes:
───────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
-Architecture: x32
-Version: 1.2-3
+Architecture: sh4
+Version: 1.2-4
Distribution: sid
Urgency: medium
-Maintainer: Debian/x32 buildd <buildd at vs76.physik.fu-berlin.de>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Maintainer: debian/sh4 buildd <buildd-vs94 at glaubitz.dialup.fu-berlin.de>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- c9030f2eb987aae2f9ba2f1b7955677e0d07078c 393918 samtools_1.2-3_x32.deb
+ 16da434bb353ef5709e176d5e5821c12ee65281b 401466 samtools_1.2-4_sh4.deb
Checksums-Sha256:
- 208e9f733ec483a03337e5ed9b55ecc43e68ee279515cf900fb6e43d344baf3a 393918 samtools_1.2-3_x32.deb
+ bc30b6384816635d6bc1bf17343c0d8ce993f7417ffcf221eb57b2e99714d948 401466 samtools_1.2-4_sh4.deb
Files:
- 5a44c515ed4b9d51d3acf9636d1f15cf 393918 science optional samtools_1.2-3_x32.deb
+ d3cbcc9d2da78ed5b38b17e34fb339aa 401466 science optional samtools_1.2-4_sh4.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_x32.deb
+samtools_1.2-4_sh4.deb
──────────────────────
new debian package, version 2.0.
- size 393918 bytes: control archive=1486 bytes.
- 801 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 401466 bytes: control archive=1609 bytes.
+ 805 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
- Architecture: x32
+ Version: 1.2-4
+ Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1043
- Depends: libc6 (>= 2.16), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 873
+ Depends: libc6 (>= 2.21), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -689,44 +752,51 @@ samtools_1.2-3_x32.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 18:50 ./
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/bin/
--rwxr-xr-x root/root 17912 2015-09-22 18:50 ./usr/bin/ace2sam
+ one 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 2016-01-14 16:54 ./
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/
+drwxr-xr-x root/root 0 2016-01-14 16:54 ./usr/bin/
+-rwxr-xr-x root/root 13652 2016-01-14 16:54 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 16:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 16:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 16:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 16:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 13776 2015-09-22 18:50 ./usr/bin/md5fa
--rwxr-xr-x root/root 9624 2015-09-22 18:50 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 9544 2016-01-14 16:54 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9544 2016-01-14 16:54 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13640 2016-01-14 16:54 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9516 2016-01-14 16:54 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 16:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 16:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 16:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 16:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 797680 2015-09-22 18:50 ./usr/bin/samtools
+-rwxr-xr-x root/root 620764 2016-01-14 16:54 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 16:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 16:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 16:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 16:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 18000 2015-09-22 18:50 ./usr/bin/wgsim
+-rwxr-xr-x root/root 17812 2016-01-14 16:54 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 16:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 16:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/share/
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-01-14 16:54 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 16:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 16:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 16:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 16:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 16:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 18:50 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 13:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 13:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 13:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 13:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 13:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-01-14 16:53 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-01-14 16:54 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-01-14 16:53 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2016-01-14 16:53 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-01-14 16:53 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-01-14 16:53 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -745,24 +815,24 @@ Not cleaning session: cloned chroot in use
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Build Architecture: x32
-Build-Space: 14968
-Build-Time: 39
+Build Architecture: sh4
+Build-Space: 14728
+Build-Time: 697
Distribution: sid
-Host Architecture: x32
-Install-Time: 22
-Job: samtools_1.2-3
+Host Architecture: sh4
+Install-Time: 201
+Job: samtools_1.2-4
Machine Architecture: amd64
Package: samtools
-Package-Time: 79
-Source-Version: 1.2-3
-Space: 14968
+Package-Time: 980
+Source-Version: 1.2-4
+Space: 14728
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1850
-Build needed 00:01:19, 14968k disc space
-Signature with key 'A644D214' requested:
- signfile /var/lib/buildd/build/samtools_1.2-3_x32.changes A644D214
+Finished at 20160114-1654
+Build needed 00:16:20, 14728k disc space
+Signature with key '933A5126' requested:
+ signfile /var/lib/buildd/build/samtools_1.2-4_sh4.changes 933A5126
Successfully signed changes file
diff --git a/x32.log b/x32.log
index 9e4d453..0dcc8b3 100644
--- a/x32.log
+++ b/x32.log
@@ -2,64 +2,61 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs76.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-3 (x32) 22 Sep 2015 18:49 ║
+║ samtools 1.2-4 (x32) 21 Dec 2015 15:57 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-3
-Source Version: 1.2-3
+Version: 1.2-4
+Source Version: 1.2-4
Distribution: sid
Machine Architecture: amd64
Host Architecture: x32
Build Architecture: x32
-I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7' with '«CHROOT»'
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+I: NOTICE: Log filtering will replace 'build/samtools-p0nYDh/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-p0nYDh' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-0887497a-406f-4ea7-b28f-712fd7874df5' with '«CHROOT»'
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org unstable InRelease [253 kB]
-Get:2 http://incoming.debian.org buildd-unstable InRelease [111 kB]
-Get:3 http://incoming.debian.org buildd-unstable/main Sources [353 kB]
-Get:4 http://ftp.debian.org unstable/main Sources/DiffIndex [7876 B]
-Get:5 http://ftp.debian-ports.org unstable InRelease [41.0 kB]
-Ign http://incoming.debian-ports.org unstable InRelease
-Get:6 http://ftp.debian.org unstable/main 2015-09-17-1433.22.pdiff [18.3 kB]
-Get:7 http://ftp.debian.org unstable/main 2015-09-17-2033.47.pdiff [17.0 kB]
-Get:8 http://ftp.debian.org unstable/main 2015-09-18-0236.10.pdiff [2554 B]
-Get:9 http://ftp.debian.org unstable/main 2015-09-18-0836.19.pdiff [3115 B]
-Get:10 http://ftp.debian.org unstable/main 2015-09-18-1434.45.pdiff [20.1 kB]
-Get:11 http://incoming.debian-ports.org unstable Release.gpg [836 B]
-Get:12 http://ftp.debian.org unstable/main 2015-09-18-2038.10.pdiff [8273 B]
-Get:13 http://ftp.debian.org unstable/main 2015-09-19-0234.31.pdiff [15.8 kB]
-Get:14 http://ftp.debian-ports.org unreleased InRelease [44.8 kB]
-Get:15 http://ftp.debian.org unstable/main 2015-09-19-0836.28.pdiff [5086 B]
-Get:16 http://ftp.debian.org unstable/main 2015-09-19-1440.27.pdiff [12.2 kB]
-Get:17 http://ftp.debian.org unstable/main 2015-09-19-2034.22.pdiff [28.8 kB]
-Get:18 http://ftp.debian.org unstable/main 2015-09-20-0235.43.pdiff [10.9 kB]
-Get:19 http://incoming.debian-ports.org unstable Release [39.6 kB]
-Get:20 http://ftp.debian.org unstable/main 2015-09-20-0846.24.pdiff [2176 B]
-Get:21 http://ftp.debian.org unstable/main 2015-09-20-1435.54.pdiff [11.3 kB]
-Get:22 http://ftp.debian.org unstable/main 2015-09-20-2047.32.pdiff [10.4 kB]
-Get:23 http://ftp.debian.org unstable/main 2015-09-21-0236.32.pdiff [8959 B]
-Get:24 http://ftp.debian.org unstable/main 2015-09-21-0835.50.pdiff [4865 B]
-Get:25 http://ftp.debian.org unstable/main 2015-09-21-1436.46.pdiff [17.2 kB]
-Get:26 http://ftp.debian.org unstable/main 2015-09-21-2043.02.pdiff [12.8 kB]
-Get:27 http://ftp.debian-ports.org unstable/main x32 Packages [13.0 MB]
-Get:28 http://ftp.debian.org unstable/main 2015-09-22-0237.33.pdiff [10.4 kB]
-Get:29 http://ftp.debian.org unstable/main 2015-09-22-0834.54.pdiff [6855 B]
-Get:30 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
-Get:31 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
-Get:32 http://incoming.debian-ports.org unstable/main x32 Packages [36.7 kB]
-Ign http://incoming.debian-ports.org unstable/main Translation-en
-Get:33 http://ftp.debian-ports.org unreleased/main x32 Packages [63.0 kB]
-Ign http://ftp.debian-ports.org unstable/main Translation-en
-Ign http://ftp.debian-ports.org unreleased/main Translation-en
-Fetched 14.2 MB in 10s (1346 kB/s)
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Ign:3 http://incoming.debian-ports.org/buildd unstable InRelease
+Get:4 http://ftp.debian-ports.org/debian unstable InRelease [41.5 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources.diff/Index [26.1 kB]
+Get:6 http://ftp.debian.org/debian unstable/main Sources 2015-12-20-2100.56.pdiff [22.2 kB]
+Get:7 http://incoming.debian-ports.org/buildd unstable Release [43.8 kB]
+Get:8 http://ftp.debian.org/debian unstable/main Sources 2015-12-21-0248.49.pdiff [22.2 kB]
+Get:9 http://ftp.debian.org/debian unstable/main Sources 2015-12-21-0844.33.pdiff [13.8 kB]
+Get:9 http://ftp.debian.org/debian unstable/main Sources 2015-12-21-0844.33.pdiff [13.8 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [199 kB]
+Get:11 http://ftp.debian-ports.org/debian unreleased InRelease [47.8 kB]
+Get:12 http://incoming.debian-ports.org/buildd unstable Release.gpg [836 B]
+Get:13 http://ftp.debian-ports.org/debian unstable/main x32 Packages [13.7 MB]
+Get:14 http://incoming.debian-ports.org/buildd unstable/main x32 Packages [78.2 kB]
+Fetched 14.6 MB in 21s (687 kB/s)
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -70,20 +67,25 @@ Check APT
─────────
Checking available source versions...
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Download source files with APT
──────────────────────────────
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4330 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
-Fetched 4330 kB in 2s (1775 kB/s)
+Please use:
+git clone git://anonscm.debian.org/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 4332 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (dsc) [2116 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.2-4 (diff) [11.5 kB]
+Fetched 4332 kB in 8s (529 kB/s)
Download complete and in download only mode
Check architectures
@@ -93,15 +95,34 @@ Check architectures
Check dependencies
──────────────────
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ba45YF/apt_archive/sbuild-build-depends-core-dummy.deb'.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-Ef3l6_/apt_archive/sbuild-build-depends-core-dummy.deb'.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
OK
-Ign file: ./ InRelease
-Get:1 file: ./ Release.gpg [299 B]
-Get:2 file: ./ Release [2119 B]
-Ign file: ./ Translation-en
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+Get:1 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ Packages [523 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -109,22 +130,24 @@ Reading package lists...
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Reading package lists...
Building dependency tree...
Reading state information...
-The following extra packages will be installed:
+The following additional packages will be installed:
fakeroot libfakeroot
The following NEW packages will be installed:
fakeroot libfakeroot sbuild-build-depends-core-dummy
-0 upgraded, 3 newly installed, 0 to remove and 24 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded.
Need to get 129 kB/130 kB of archives.
After this operation, 411 kB of additional disk space will be used.
-Get:1 http://ftp.debian-ports.org/debian/ unstable/main libfakeroot x32 1.20.2-1 [44.8 kB]
-Get:2 http://ftp.debian-ports.org/debian/ unstable/main fakeroot x32 1.20.2-1 [84.6 kB]
+Get:1 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
+Get:2 http://ftp.debian-ports.org/debian unstable/main x32 libfakeroot x32 1.20.2-1 [44.8 kB]
+Get:3 http://ftp.debian-ports.org/debian unstable/main x32 fakeroot x32 1.20.2-1 [84.6 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 129 kB in 1s (115 kB/s)
+Fetched 129 kB in 1s (110 kB/s)
Selecting previously unselected package libfakeroot:x32.
-(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 ... 12802 files and directories currently installed.)
+(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 ... 12692 files and directories currently installed.)
Preparing to unpack .../libfakeroot_1.20.2-1_x32.deb ...
Unpacking libfakeroot:x32 (1.20.2-1) ...
Selecting previously unselected package fakeroot.
@@ -137,15 +160,37 @@ Setting up libfakeroot:x32 (1.20.2-1) ...
Setting up fakeroot (1.20.2-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
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-7knP0Q/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-0SHSGc/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
OK
-Ign file: ./ InRelease
-Get:1 file: ./ Release.gpg [299 B]
-Get:2 file: ./ Release [2119 B]
-Ign file: ./ Translation-en
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+Get:1 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Sources [471 B]
+Get:5 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ Packages [729 B]
Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -153,100 +198,109 @@ Reading package lists...
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Reading package lists...
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 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
+The following additional packages will be installed:
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf tabix
+ zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ 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 libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
+ 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 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 24 not upgraded.
-Need to get 18.3 MB/18.3 MB of archives.
-After this operation, 64.0 MB of additional disk space will be used.
-Get:1 http://ftp.debian-ports.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp.debian-ports.org/debian/ unstable/main groff-base x32 1.22.3-1 [1199 kB]
-Get:3 http://ftp.debian-ports.org/debian/ unstable/main bsdmainutils x32 9.0.6 [183 kB]
-Get:4 http://ftp.debian-ports.org/debian/ unstable/main libpipeline1 x32 1.4.1-1 [28.0 kB]
-Get:5 http://ftp.debian-ports.org/debian/ unstable/main man-db x32 2.7.3-1 [1003 kB]
-Get:6 http://ftp.debian-ports.org/debian/ unstable/main libffi6 x32 3.2.1-3 [19.9 kB]
-Get:7 http://ftp.debian-ports.org/debian/ unstable/main libunistring0 x32 0.9.3-5.2 [289 kB]
-Get:8 http://ftp.debian-ports.org/debian/ unstable/main libmagic1 x32 1:5.25-1 [256 kB]
-Get:9 http://ftp.debian-ports.org/debian/ unstable/main file x32 1:5.25-1 [61.5 kB]
-Get:10 http://ftp.debian-ports.org/debian/ unstable/main gettext-base x32 0.19.6-1 [123 kB]
-Get:11 http://ftp.debian-ports.org/debian/ unstable/main libicu55 x32 55.1-5 [7659 kB]
-Get:12 http://ftp.debian-ports.org/debian/ unstable/main libxml2 x32 2.9.2+zdfsg1-4 [924 kB]
-Get:13 http://ftp.debian-ports.org/debian/ unstable/main libglib2.0-0 x32 2.44.1-1.1 [2471 kB]
-Get:14 http://ftp.debian-ports.org/debian/ unstable/main libcroco3 x32 0.6.8-3+b1 [135 kB]
-Get:15 http://ftp.debian-ports.org/debian/ unstable/main gettext x32 0.19.6-1 [1466 kB]
-Get:16 http://ftp.debian-ports.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:17 http://ftp.debian-ports.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
-Get:18 http://ftp.debian-ports.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
-Get:19 http://ftp.debian-ports.org/debian/ unstable/main libhts1 x32 1.2.1-1 [226 kB]
-Get:20 http://ftp.debian-ports.org/debian/ unstable/main libhts-dev x32 1.2.1-1 [274 kB]
-Get:21 http://ftp.debian-ports.org/debian/ unstable/main libio-pty-perl x32 1:1.08-1+b2 [36.0 kB]
-Get:22 http://ftp.debian-ports.org/debian/ unstable/main libtinfo-dev x32 6.0+20150810-1 [76.5 kB]
-Get:23 http://ftp.debian-ports.org/debian/ unstable/main libncurses5-dev x32 6.0+20150810-1 [170 kB]
-Get:24 http://ftp.debian-ports.org/debian/ unstable/main tabix x32 1.2.1-1 [221 kB]
-Get:25 http://ftp.debian-ports.org/debian/ unstable/main zlib1g-dev x32 1:1.2.8.dfsg-2+b1 [206 kB]
+ bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
+ libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded.
+Need to get 18.6 MB/18.6 MB of archives.
+After this operation, 64.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-0SHSGc/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [974 B]
+Get:2 http://ftp.debian-ports.org/debian unstable/main x32 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.debian-ports.org/debian unstable/main x32 groff-base x32 1.22.3-4 [1149 kB]
+Get:4 http://ftp.debian-ports.org/debian unstable/main x32 bsdmainutils x32 9.0.6+b1 [183 kB]
+Get:5 http://ftp.debian-ports.org/debian unstable/main x32 libpipeline1 x32 1.4.1-1 [28.0 kB]
+Get:6 http://ftp.debian-ports.org/debian unstable/main x32 man-db x32 2.7.5-1 [1004 kB]
+Get:7 http://ftp.debian-ports.org/debian unstable/main x32 libunistring0 x32 0.9.3-5.2 [289 kB]
+Get:8 http://ftp.debian-ports.org/debian unstable/main x32 libmagic1 x32 1:5.25-2 [256 kB]
+Get:9 http://ftp.debian-ports.org/debian unstable/main x32 file x32 1:5.25-2 [61.5 kB]
+Get:10 http://ftp.debian-ports.org/debian unstable/main x32 gettext-base x32 0.19.6-1 [123 kB]
+Get:11 http://ftp.debian-ports.org/debian unstable/main x32 libicu55 x32 55.1-6 [7656 kB]
+Get:12 http://ftp.debian-ports.org/debian unstable/main x32 libxml2 x32 2.9.3+dfsg1-1 [928 kB]
+Get:13 http://ftp.debian-ports.org/debian unstable/main x32 libffi6 x32 3.2.1-4 [20.1 kB]
+Get:14 http://ftp.debian-ports.org/debian unstable/main x32 libglib2.0-0 x32 2.46.2-1 [2648 kB]
+Get:15 http://ftp.debian-ports.org/debian unstable/main x32 libcroco3 x32 0.6.11-1 [144 kB]
+Get:16 http://ftp.debian-ports.org/debian unstable/main x32 gettext x32 0.19.6-1 [1466 kB]
+Get:17 http://ftp.debian-ports.org/debian unstable/main x32 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:18 http://ftp.debian-ports.org/debian unstable/main x32 po-debconf all 1.0.18 [248 kB]
+Get:19 http://ftp.debian-ports.org/debian unstable/main x32 libarchive-zip-perl all 1.55-1 [97.4 kB]
+Get:20 http://ftp.debian-ports.org/debian unstable/main x32 libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
+Get:21 http://ftp.debian-ports.org/debian unstable/main x32 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:22 http://ftp.debian-ports.org/debian unstable/main x32 dh-strip-nondeterminism all 0.014-1 [7472 B]
+Get:23 http://ftp.debian-ports.org/debian unstable/main x32 debhelper all 9.20151220 [830 kB]
+Get:24 http://ftp.debian-ports.org/debian unstable/main x32 libhts1 x32 1.2.1-2 [225 kB]
+Get:25 http://ftp.debian-ports.org/debian unstable/main x32 libhts-dev x32 1.2.1-2 [274 kB]
+Get:26 http://ftp.debian-ports.org/debian unstable/main x32 libio-pty-perl x32 1:1.08-1.1+b1 [33.8 kB]
+Get:27 http://ftp.debian-ports.org/debian unstable/main x32 libtinfo-dev x32 6.0+20151024-2 [76.5 kB]
+Get:28 http://ftp.debian-ports.org/debian unstable/main x32 libncurses5-dev x32 6.0+20151024-2 [173 kB]
+Get:29 http://ftp.debian-ports.org/debian unstable/main x32 tabix x32 1.2.1-2 [220 kB]
+Get:30 http://ftp.debian-ports.org/debian unstable/main x32 zlib1g-dev x32 1:1.2.8.dfsg-2+b2 [204 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.3 MB in 10s (1822 kB/s)
+Fetched 18.6 MB in 5s (3273 kB/s)
Selecting previously unselected package bash-completion.
-(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 ... 12852 files and directories currently installed.)
+(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 ... 12741 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_x32.deb ...
-Unpacking groff-base (1.22.3-1) ...
+Preparing to unpack .../groff-base_1.22.3-4_x32.deb ...
+Unpacking groff-base (1.22.3-4) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_x32.deb ...
-Unpacking bsdmainutils (9.0.6) ...
+Preparing to unpack .../bsdmainutils_9.0.6+b1_x32.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
Selecting previously unselected package libpipeline1:x32.
Preparing to unpack .../libpipeline1_1.4.1-1_x32.deb ...
Unpacking libpipeline1:x32 (1.4.1-1) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_x32.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:x32.
-Preparing to unpack .../libffi6_3.2.1-3_x32.deb ...
-Unpacking libffi6:x32 (3.2.1-3) ...
+Preparing to unpack .../man-db_2.7.5-1_x32.deb ...
+Unpacking man-db (2.7.5-1) ...
Selecting previously unselected package libunistring0:x32.
Preparing to unpack .../libunistring0_0.9.3-5.2_x32.deb ...
Unpacking libunistring0:x32 (0.9.3-5.2) ...
Selecting previously unselected package libmagic1:x32.
-Preparing to unpack .../libmagic1_1%3a5.25-1_x32.deb ...
-Unpacking libmagic1:x32 (1:5.25-1) ...
+Preparing to unpack .../libmagic1_1%3a5.25-2_x32.deb ...
+Unpacking libmagic1:x32 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-1_x32.deb ...
-Unpacking file (1:5.25-1) ...
+Preparing to unpack .../file_1%3a5.25-2_x32.deb ...
+Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.6-1_x32.deb ...
Unpacking gettext-base (0.19.6-1) ...
Selecting previously unselected package libicu55:x32.
-Preparing to unpack .../libicu55_55.1-5_x32.deb ...
-Unpacking libicu55:x32 (55.1-5) ...
+Preparing to unpack .../libicu55_55.1-6_x32.deb ...
+Unpacking libicu55:x32 (55.1-6) ...
Selecting previously unselected package libxml2:x32.
-Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_x32.deb ...
-Unpacking libxml2:x32 (2.9.2+zdfsg1-4) ...
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_x32.deb ...
+Unpacking libxml2:x32 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libffi6:x32.
+Preparing to unpack .../libffi6_3.2.1-4_x32.deb ...
+Unpacking libffi6:x32 (3.2.1-4) ...
Selecting previously unselected package libglib2.0-0:x32.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_x32.deb ...
-Unpacking libglib2.0-0:x32 (2.44.1-1.1) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-1_x32.deb ...
+Unpacking libglib2.0-0:x32 (2.46.2-1) ...
Selecting previously unselected package libcroco3:x32.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_x32.deb ...
-Unpacking libcroco3:x32 (0.6.8-3+b1) ...
+Preparing to unpack .../libcroco3_0.6.11-1_x32.deb ...
+Unpacking libcroco3:x32 (0.6.11-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../gettext_0.19.6-1_x32.deb ...
Unpacking gettext (0.19.6-1) ...
@@ -256,72 +310,92 @@ 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 libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.55-1_all.deb ...
+Unpacking libarchive-zip-perl (1.55-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.014-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.014-1) ...
+Selecting previously unselected package libtimedate-perl.
+Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
+Unpacking libtimedate-perl (2.3000-2) ...
+Selecting previously unselected package dh-strip-nondeterminism.
+Preparing to unpack .../dh-strip-nondeterminism_0.014-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.014-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
+Preparing to unpack .../debhelper_9.20151220_all.deb ...
+Unpacking debhelper (9.20151220) ...
Selecting previously unselected package libhts1:x32.
-Preparing to unpack .../libhts1_1.2.1-1_x32.deb ...
-Unpacking libhts1:x32 (1.2.1-1) ...
+Preparing to unpack .../libhts1_1.2.1-2_x32.deb ...
+Unpacking libhts1:x32 (1.2.1-2) ...
Selecting previously unselected package libhts-dev:x32.
-Preparing to unpack .../libhts-dev_1.2.1-1_x32.deb ...
-Unpacking libhts-dev:x32 (1.2.1-1) ...
+Preparing to unpack .../libhts-dev_1.2.1-2_x32.deb ...
+Unpacking libhts-dev:x32 (1.2.1-2) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b2_x32.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b2) ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_x32.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:x32.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_x32.deb ...
-Unpacking libtinfo-dev:x32 (6.0+20150810-1) ...
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_x32.deb ...
+Unpacking libtinfo-dev:x32 (6.0+20151024-2) ...
Selecting previously unselected package libncurses5-dev:x32.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_x32.deb ...
-Unpacking libncurses5-dev:x32 (6.0+20150810-1) ...
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_x32.deb ...
+Unpacking libncurses5-dev:x32 (6.0+20151024-2) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.2.1-1_x32.deb ...
-Unpacking tabix (1.2.1-1) ...
+Preparing to unpack .../archives/tabix_1.2.1-2_x32.deb ...
+Unpacking tabix (1.2.1-2) ...
Selecting previously unselected package zlib1g-dev:x32.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_x32.deb ...
-Unpacking zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b2_x32.deb ...
+Unpacking zlib1g-dev:x32 (1:1.2.8.dfsg-2+b2) ...
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) ...
+Processing triggers for libc-bin (2.21-4) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
+Setting up groff-base (1.22.3-4) ...
+Setting up bsdmainutils (9.0.6+b1) ...
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 libpipeline1:x32 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
+Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:x32 (3.2.1-3) ...
Setting up libunistring0:x32 (0.9.3-5.2) ...
-Setting up libmagic1:x32 (1:5.25-1) ...
-Setting up file (1:5.25-1) ...
+Setting up libmagic1:x32 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.6-1) ...
-Setting up libicu55:x32 (55.1-5) ...
-Setting up libxml2:x32 (2.9.2+zdfsg1-4) ...
-Setting up libglib2.0-0:x32 (2.44.1-1.1) ...
+Setting up libicu55:x32 (55.1-6) ...
+Setting up libxml2:x32 (2.9.3+dfsg1-1) ...
+Setting up libffi6:x32 (3.2.1-4) ...
+Setting up libglib2.0-0:x32 (2.46.2-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:x32 (0.6.8-3+b1) ...
+Setting up libcroco3:x32 (0.6.11-1) ...
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 (9.20150811) ...
-Setting up libhts1:x32 (1.2.1-1) ...
-Setting up libhts-dev:x32 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b2) ...
-Setting up libtinfo-dev:x32 (6.0+20150810-1) ...
-Setting up libncurses5-dev:x32 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
-Setting up zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Setting up libarchive-zip-perl (1.55-1) ...
+Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:x32 (1.2.1-2) ...
+Setting up libhts-dev:x32 (1.2.1-2) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:x32 (6.0+20151024-2) ...
+Setting up libncurses5-dev:x32 (6.0+20151024-2) ...
+Setting up tabix (1.2.1-2) ...
+Setting up zlib1g-dev:x32 (1:1.2.8.dfsg-2+b2) ...
+Setting up debhelper (9.20151220) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
+Setting up dh-strip-nondeterminism (0.014-1) ...
+Processing triggers for libc-bin (2.21-4) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-17 gcc-4.9_4.9.3-4 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-4.9-dev_4.9.3-4 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_2.25.1-1 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-4.9_4.9.3-4 cpp-5_5.2.1-17 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42. [...]
+Kernel: Linux 4.1.0-0.bpo.2-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-4 gcc-5_5.3.1-4 libc6-dev_2.21-4 libstdc++-5-dev_5.3.1-4 libstdc++6_5.3.1-4 linux-libc-dev_4.3.3-2
+Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.3.1-1 cpp-5_5.3.1-4 dash_0.5.7-4 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20151220 debian-archive-keyring_2014.3 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e2fs [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -331,25 +405,31 @@ Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5
Unpack source
─────────────
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-3.debian.tar.xz
+dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
+dpkg-source: info: applying mayhem.patch
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Check disc space
────────────────
Sufficient free space for build
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
User Environment
────────────────
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
DEB_BUILD_OPTIONS=nobench nocheck
HOME=/sbuild-nonexistent
LD_LIBRARY_PATH=/usr/lib/libeatmydata
@@ -362,18 +442,20 @@ SCHROOT_CHROOT_NAME=sid-x32-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7
+SCHROOT_SESSION_ID=sid-x32-sbuild-0887497a-406f-4ea7-b28f-712fd7874df5
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c20511
+XDG_RUNTIME_DIR=/run/user/114
+XDG_SESSION_ID=18355
dpkg-buildpackage
─────────────────
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture x32
@@ -542,6 +624,9 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/
+ cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
+ cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
@@ -557,14 +642,27 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
+ man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
+ chmod 644 ace2sam.1.new
+ mv -f ace2sam.1.new ace2sam.1
+ man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
+ chmod 644 samtools.pl.1.new
+ mv -f samtools.pl.1.new samtools.pl.1
+ man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
+ dh_lintian -a -O--parallel
+ install -d debian/samtools/usr/share/lintian/overrides
+ install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
+ dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
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
+ chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
+ gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
@@ -572,31 +670,67 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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-gnux32/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/lib/x86_64-linux-gnux32/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
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/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4b
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4b/23758064cd64d8a1e143a84fd34a59f0f18c19.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4b/23758064cd64d8a1e143a84fd34a59f0f18c19.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/4b/23758064cd64d8a1e143a84fd34a59f0f18c19.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d2
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d2/dbabaf7b4e33eeab808e691411e0c97777a95c.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d2/dbabaf7b4e33eeab808e691411e0c97777a95c.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d2/dbabaf7b4e33eeab808e691411e0c97777a95c.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d5
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d5/9bd079968392ffaaaa51b97abc05aed198a42b.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d5/9bd079968392ffaaaa51b97abc05aed198a42b.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/d5/9bd079968392ffaaaa51b97abc05aed198a42b.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/47
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/47/b0d26c7fed38a9ada9e98c4a111b60d614d80d.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/47/b0d26c7fed38a9ada9e98c4a111b60d614d80d.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/47/b0d26c7fed38a9ada9e98c4a111b60d614d80d.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/22
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/22/0268873d32598d4683e1828ade81b23b6c5a45.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/22/0268873d32598d4683e1828ade81b23b6c5a45.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/22/0268873d32598d4683e1828ade81b23b6c5a45.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/8d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/8d/97e0b93b2f815fb4fd3509599881148bafd02a.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/8d/97e0b93b2f815fb4fd3509599881148bafd02a.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/8d/97e0b93b2f815fb4fd3509599881148bafd02a.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/03
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/03/696d095f2c8ba9d709bc3d78da28f0fe752d0d.debug
+ chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/03/696d095f2c8ba9d709bc3d78da28f0fe752d0d.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/03/696d095f2c8ba9d709bc3d78da28f0fe752d0d.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
+ install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=03696d095f2c8ba9d709bc3d78da28f0fe752d0d 220268873d32598d4683e1828ade81b23b6c5a45 47b0d26c7fed38a9ada9e98c4a111b60d6 [...]
+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 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
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}
@@ -606,21 +740,28 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
(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/.debhelper/samtools/ddeb-root >/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/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_x32.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-3_x32.deb'.
- dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.2-3_x32.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-4_x32.deb'.
+ dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.2-4_x32.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150922-1850
+Build finished at 20151221-1559
Finished
────────
I: Built successfully
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
@@ -632,54 +773,107 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_x32.changes:
+samtools_1.2-4_x32.changes:
───────────────────────────
Format: 1.8
-Date: Tue, 22 Sep 2015 06:42:01 -0700
+Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: x32
-Version: 1.2-3
+Version: 1.2-4
Distribution: sid
Urgency: medium
Maintainer: Debian/x32 buildd <buildd at vs76.physik.fu-berlin.de>
-Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Changed-By: Andreas Tille <tille at debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
- samtools-test - test files for the samtools package.
-Closes: 799698
+ samtools-test - test files for the samtools package
+Closes: 716197 716199
Changes:
- samtools (1.2-3) unstable; urgency=medium
+ samtools (1.2-4) unstable; urgency=medium
.
- * Team upload.
- [19de55e] Revert "Allow all scripts to be called without language extensions"
- (Closes: #799698)
- [658179c] Revert "Remove source files not present in upstream tarball"
+ * Team upload
+ * Fix synopsis
+ * Fix Vcs-Browser
+ * Add lintian-override to document that the language extensions are used
+ internally
+ * Fix spelling
+ * Fix Mayhem issues caused by unlimited reads of gz input
+ Closes: #716199, #716197
+ * Provide some more manpages
Checksums-Sha1:
- c9030f2eb987aae2f9ba2f1b7955677e0d07078c 393918 samtools_1.2-3_x32.deb
+ 6008a94a46547075945de1803f65a49eb0abc070 400108 samtools-dbgsym_1.2-4_x32.deb
+ 84fe7a2cb520a82fe58c55080030b3b1a189f096 394188 samtools_1.2-4_x32.deb
Checksums-Sha256:
- 208e9f733ec483a03337e5ed9b55ecc43e68ee279515cf900fb6e43d344baf3a 393918 samtools_1.2-3_x32.deb
+ 3b3f8c650c590a483e36149ac79a201dd2d1e4cafd96a2bc9f60a2adc06998c6 400108 samtools-dbgsym_1.2-4_x32.deb
+ 53cd76579dbf55718aa41dd1feea82b9f5fb22ad991830a40e0cdce342af8ba1 394188 samtools_1.2-4_x32.deb
Files:
- 5a44c515ed4b9d51d3acf9636d1f15cf 393918 science optional samtools_1.2-3_x32.deb
+ 23f3b6f007f9461e5ea34917bdef64c1 400108 debug extra samtools-dbgsym_1.2-4_x32.deb
+ b5bbf799311fccfbc4d00fa1460690e3 394188 science optional samtools_1.2-4_x32.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-3_x32.deb
+samtools-dbgsym_1.2-4_x32.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 400108 bytes: control archive=812 bytes.
+ 644 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.2-4
+ Architecture: x32
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 466
+ Depends: samtools (= 1.2-4)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 03696d095f2c8ba9d709bc3d78da28f0fe752d0d 220268873d32598d4683e1828ade81b23b6c5a45 47b0d26c7fed38a9ada9e98c4a111b60d614d80d 4b23758064cd64d8a1e143a84fd34a59f0f18c19 8d97e0b93b2f815fb4fd3509599881148bafd02a d2dbabaf7b4e33eeab808e691411e0c97777a95c d59bd079968392ffaaaa51b97abc05aed198a42b
+
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/03/
+-rw-r--r-- root/root 16332 2015-12-21 15:59 ./usr/lib/debug/.build-id/03/696d095f2c8ba9d709bc3d78da28f0fe752d0d.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/22/
+-rw-r--r-- root/root 12300 2015-12-21 15:59 ./usr/lib/debug/.build-id/22/0268873d32598d4683e1828ade81b23b6c5a45.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/47/
+-rw-r--r-- root/root 9744 2015-12-21 15:59 ./usr/lib/debug/.build-id/47/b0d26c7fed38a9ada9e98c4a111b60d614d80d.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/4b/
+-rw-r--r-- root/root 381496 2015-12-21 15:59 ./usr/lib/debug/.build-id/4b/23758064cd64d8a1e143a84fd34a59f0f18c19.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/8d/
+-rw-r--r-- root/root 9596 2015-12-21 15:59 ./usr/lib/debug/.build-id/8d/97e0b93b2f815fb4fd3509599881148bafd02a.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/d2/
+-rw-r--r-- root/root 17672 2015-12-21 15:59 ./usr/lib/debug/.build-id/d2/dbabaf7b4e33eeab808e691411e0c97777a95c.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/lib/debug/.build-id/d5/
+-rw-r--r-- root/root 9732 2015-12-21 15:59 ./usr/lib/debug/.build-id/d5/9bd079968392ffaaaa51b97abc05aed198a42b.debug
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2015-12-21 15:59 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.2-4_x32.deb
──────────────────────
new debian package, version 2.0.
- size 393918 bytes: control archive=1486 bytes.
- 801 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
+ size 394188 bytes: control archive=1607 bytes.
+ 806 bytes, 17 lines control
+ 1828 bytes, 31 lines md5sums
Package: samtools
- Version: 1.2-3
+ Version: 1.2-4
Architecture: x32
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1043
+ Installed-Size: 1042
Depends: libc6 (>= 2.16), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -689,44 +883,51 @@ samtools_1.2-3_x32.deb
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
- 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 2015-09-22 18:50 ./
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/bin/
--rwxr-xr-x root/root 17912 2015-09-22 18:50 ./usr/bin/ace2sam
+ one 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 2015-12-21 15:59 ./
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/bin/
+-rwxr-xr-x root/root 18056 2015-12-21 15:59 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2015-02-02 16:18 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2015-02-02 16:18 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2015-02-02 16:18 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2015-02-02 16:18 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 13776 2015-09-22 18:50 ./usr/bin/md5fa
--rwxr-xr-x root/root 9624 2015-09-22 18:50 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 9832 2015-12-21 15:59 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9832 2015-12-21 15:59 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13920 2015-12-21 15:59 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9768 2015-12-21 15:59 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2015-02-02 16:18 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48036 2015-02-02 16:18 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2015-02-02 16:18 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2015-02-02 16:18 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 797680 2015-09-22 18:50 ./usr/bin/samtools
+-rwxr-xr-x root/root 789640 2015-12-21 15:59 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2015-02-02 16:18 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2015-02-02 16:18 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2015-02-02 16:18 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2015-02-02 16:18 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 18000 2015-09-22 18:50 ./usr/bin/wgsim
+-rwxr-xr-x root/root 18144 2015-12-21 15:59 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 16:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 16:18 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/samtools/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 16:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-22 16:07 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3629 2015-09-22 16:07 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-22 16:07 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-22 16:07 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-22 18:50 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 1031 2015-12-21 13:50 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3792 2015-12-21 13:50 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-12-21 13:50 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-12-21 13:50 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2015-12-21 13:50 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-12-21 15:59 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2015-12-21 15:59 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 12907 2015-12-21 15:59 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2015-12-21 15:59 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2015-12-21 15:59 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -739,30 +940,34 @@ drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/man1/
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
Not cleaning session: cloned chroot in use
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
+W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name ‘source-root-users’ is not a permitted name.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: x32
-Build-Space: 14968
-Build-Time: 39
+Build-Space: 15852
+Build-Time: 41
Distribution: sid
Host Architecture: x32
Install-Time: 22
-Job: samtools_1.2-3
+Job: samtools_1.2-4
Machine Architecture: amd64
Package: samtools
-Package-Time: 79
-Source-Version: 1.2-3
-Space: 14968
+Package-Time: 99
+Source-Version: 1.2-4
+Space: 15852
Status: successful
-Version: 1.2-3
+Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
-Finished at 20150922-1850
-Build needed 00:01:19, 14968k disc space
+Finished at 20151221-1559
+Build needed 00:01:39, 15852k disc space
Signature with key 'A644D214' requested:
- signfile /var/lib/buildd/build/samtools_1.2-3_x32.changes A644D214
+ signfile /var/lib/buildd/build/samtools_1.2-4_x32.changes A644D214
Successfully signed changes file
--
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