[med-svn] samtools 03/04: Build logs for version 1.3-1.
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 9aa32f5088dacafc98ff7fdd3f1d3e4dad8205bd
Author: Charles Plessy <plessy at debian.org>
Date: Wed Apr 27 09:53:30 2016 +0900
Build logs for version 1.3-1.
---
arm64.log | 1338 ++++++++++++++++++++++++++++----------------------
armel.log | 1372 +++++++++++++++++++++++-----------------------------
i386.log | 1323 ++++++++++++++++++++++++++++----------------------
kfreebsd-amd64.log | 1319 ++++++++++++++++++++++++++++----------------------
kfreebsd-i386.log | 1320 ++++++++++++++++++++++++++++----------------------
m68k.log | 1100 ++++++++++++++++++++++++++++++++++++++---
mips64el.log | 1324 +++++++++++++++++++++++++++++---------------------
mipsel.log | 1369 +++++++++++++++++++++++----------------------------
powerpcspe.log | 795 ++++++++++++++++++++++++++++++
ppc64el.log | 1318 ++++++++++++++++++++++++++++---------------------
sh4.log | 739 +++++++++++++++-------------
x32.log | 947 ++++++++++++++++--------------------
12 files changed, 8362 insertions(+), 5902 deletions(-)
diff --git a/arm64.log b/arm64.log
index a74d73d..0d79756 100644
--- a/arm64.log
+++ b/arm64.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-arm-03.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-linaro-03.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (arm64) 21 Dec 2015 13:17 ║
+║ samtools 1.3-1 (arm64) 05 Feb 2016 16:17 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
-Machine Architecture: arm64
+Machine Architecture: armhf
Host Architecture: arm64
Build Architecture: arm64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-khk954/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-khk954' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-bf008829-8b2e-4b88-8f01-d86db0e37341' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.us.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:4 http://ftp.us.debian.org/debian unstable/main Sources [8513 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main arm64 Packages [171 kB]
+Get:9 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib arm64 Packages [1104 B]
+Get:11 http://ftp.us.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:12 http://ftp.us.debian.org/debian unstable/non-free Sources [106 kB]
+Get:13 http://ftp.us.debian.org/debian unstable/main arm64 Packages [7783 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:15 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:16 http://ftp.debian.org/debian unstable/main arm64 Packages [7783 kB]
+Get:17 http://ftp.us.debian.org/debian unstable/contrib arm64 Packages [47.0 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib arm64 Packages [47.0 kB]
+Fetched 34.1 MB in 12s (2784 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 14s (261 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-oA1tFt/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-SmTVOu/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ Packages [526 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 10 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]
+Get:1 file:/«BUILDDIR»/resolver-SmTVOu/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 ... 12165 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%
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(Reading database ... 60%
(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 ... 12179 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-FbKrJU/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-IWW4Pm/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,77 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 10 not upgraded.
+Need to get 20.0 MB/20.0 MB of archives.
+After this operation, 75.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-IWW4Pm/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 http://ftp.us.debian.org/debian unstable/main arm64 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.us.debian.org/debian unstable/main arm64 groff-base arm64 1.22.3-7 [1156 kB]
+Get:4 http://ftp.us.debian.org/debian unstable/main arm64 bsdmainutils arm64 9.0.6+b1 [178 kB]
+Get:5 http://ftp.us.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.4.1-2 [25.0 kB]
+Get:6 http://ftp.us.debian.org/debian unstable/main arm64 man-db arm64 2.7.5-1 [975 kB]
+Get:7 http://ftp.us.debian.org/debian unstable/main arm64 autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.us.debian.org/debian unstable/main arm64 libsigsegv2 arm64 2.10-4+b2 [28.5 kB]
+Get:9 http://ftp.us.debian.org/debian unstable/main arm64 libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
+Get:10 http://ftp.us.debian.org/debian unstable/main arm64 libmagic1 arm64 1:5.25-2 [248 kB]
+Get:11 http://ftp.us.debian.org/debian unstable/main arm64 file arm64 1:5.25-2 [61.5 kB]
+Get:12 http://ftp.us.debian.org/debian unstable/main arm64 gettext-base arm64 0.19.7-2 [112 kB]
+Get:13 http://ftp.us.debian.org/debian unstable/main arm64 libicu55 arm64 55.1-7 [7492 kB]
+Get:14 http://ftp.us.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.3+dfsg1-1 [785 kB]
+Get:15 http://ftp.us.debian.org/debian unstable/main arm64 m4 arm64 1.4.17-5 [244 kB]
+Get:16 http://ftp.us.debian.org/debian unstable/main arm64 autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.us.debian.org/debian unstable/main arm64 autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.us.debian.org/debian unstable/main arm64 automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.us.debian.org/debian unstable/main arm64 libffi6 arm64 3.2.1-4 [18.9 kB]
+Get:20 http://ftp.us.debian.org/debian unstable/main arm64 libglib2.0-0 arm64 2.46.2-3 [2450 kB]
+Get:21 http://ftp.us.debian.org/debian unstable/main arm64 libcroco3 arm64 0.6.11-1 [128 kB]
+Get:22 http://ftp.us.debian.org/debian unstable/main arm64 gettext arm64 0.19.7-2 [1411 kB]
+Get:23 http://ftp.us.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.us.debian.org/debian unstable/main arm64 po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.us.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.us.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.us.debian.org/debian unstable/main arm64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.us.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.us.debian.org/debian unstable/main arm64 debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.us.debian.org/debian unstable/main arm64 libhts1 arm64 1.3-1 [205 kB]
+Get:31 http://ftp.us.debian.org/debian unstable/main arm64 libhts-dev arm64 1.3-1 [273 kB]
+Get:32 http://ftp.us.debian.org/debian unstable/main arm64 libio-pty-perl arm64 1:1.08-1.1+b1 [32.3 kB]
+Get:33 http://ftp.us.debian.org/debian unstable/main arm64 libtinfo-dev arm64 6.0+20151024-2 [71.3 kB]
+Get:34 http://ftp.us.debian.org/debian unstable/main arm64 libncurses5-dev arm64 6.0+20151024-2 [163 kB]
+Get:35 http://ftp.us.debian.org/debian unstable/main arm64 tabix arm64 1.3-1 [199 kB]
+Get:36 http://ftp.us.debian.org/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 17.8 MB in 0s (33.4 MB/s)
+Fetched 20.0 MB in 6s (3012 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 25%
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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 ... 12165 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%
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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 ... 12179 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_1.22.3-4_arm64.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_arm64.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_arm64.deb ...
+Unpacking libpipeline1:arm64 (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_arm64.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:arm64.
+Preparing to unpack .../libsigsegv2_2.10-4+b2_arm64.deb ...
+Unpacking libsigsegv2:arm64 (2.10-4+b2) ...
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) ...
@@ -223,53 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_arm64.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:arm64.
-Preparing to unpack .../libicu55_55.1-6_arm64.deb ...
-Unpacking libicu55:arm64 (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_arm64.deb ...
+Unpacking libicu55:arm64 (55.1-7) ...
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 m4.
+Preparing to unpack .../archives/m4_1.4.17-5_arm64.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_arm64.deb ...
+Unpacking libglib2.0-0:arm64 (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_arm64.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:arm64.
-Preparing to unpack .../libhts1_1.2.1-2_arm64.deb ...
-Unpacking libhts1:arm64 (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_arm64.deb ...
+Unpacking libhts1:arm64 (1.3-1) ...
Selecting previously unselected package libhts-dev:arm64.
-Preparing to unpack .../libhts-dev_1.2.1-2_arm64.deb ...
-Unpacking libhts-dev:arm64 (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_arm64.deb ...
+Unpacking libhts-dev:arm64 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_arm64.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -280,59 +306,66 @@ Selecting previously unselected package libncurses5-dev:arm64.
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_1.2.1-2_arm64.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../archives/tabix_1.3-1_arm64.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:arm64 (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:arm64 (2.10-4+b2) ...
Setting up libunistring0:arm64 (0.9.3-5.2+b2) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:arm64 (55.1-7) ...
Setting up libxml2:arm64 (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:arm64 (3.2.1-4) ...
-Setting up libglib2.0-0:arm64 (2.46.2-1) ...
+Setting up libglib2.0-0:arm64 (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:arm64 (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:arm64 (1.3-1) ...
+Setting up libhts-dev:arm64 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
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_2.25.90.20151209-1 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 [...]
+Kernel: Linux 3.16.0-4-arm64 armhf (aarch64)
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -362,7 +394,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=6
+DEB_BUILD_OPTIONS=parallel=8
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
@@ -371,36 +403,43 @@ SCHROOT_CHROOT_NAME=sid-arm64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-arm64-sbuild-2faeabd1-88d2-44d2-8613-01450675fd28
+SCHROOT_SESSION_ID=sid-arm64-sbuild-bf008829-8b2e-4b88-8f01-d86db0e37341
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=c8678
+XDG_SESSION_ID=c28742
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture arm64
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j6 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j8 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -422,189 +461,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j6 HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j8 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/aarch64-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/aarch64-linux-gnu/libhts.a -lhts -lcurses -lm -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
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/aarch64-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j6 test HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j8 test 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/NsJx1DyDO8/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/T7B8QfZdHH/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NsJx1DyDO8/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NsJx1DyDO8/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NsJx1DyDO8/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/T7B8QfZdHH/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/NsJx1DyDO8/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/T7B8QfZdHH/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/NsJx1DyDO8/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/NsJx1DyDO8/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/NsJx1DyDO8/mpileup.bam.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.bam.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/T7B8QfZdHH/mpileup.bam.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/NsJx1DyDO8/mpileup.cram.list -f /tmp/NsJx1DyDO8/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/T7B8QfZdHH/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/T7B8QfZdHH/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -643,7 +737,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -673,7 +771,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -690,9 +796,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -724,6 +828,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -826,83 +934,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input) .. ok
+ 49: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
- 52: Count -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input) .. ok
+ 50: Count -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
- 53: Filter -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input) .. ok
+ 51: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
- 54: Count -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input) .. ok
+ 52: Count -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
- 55: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (SAM input).. ok
+ 53: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
- 56: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (SAM input).. ok
+ 54: Count -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
- 57: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (BAM input).. ok
+ 55: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
- 58: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (BAM input).. ok
+ 56: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
- 59: Filter -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (CRAM input).. ok
+ 57: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
- 60: Count -R /tmp/NsJx1DyDO8/view.001.fogn -r grp2 (CRAM input).. ok
+ 58: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
- 61: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input).. ok
+ 59: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
- 62: Count -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (SAM input).. ok
+ 60: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
- 63: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input).. ok
+ 61: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
- 64: Count -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (BAM input).. ok
+ 62: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
- 65: Filter -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input).. ok
+ 63: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
- 66: Count -r grp2 -R /tmp/NsJx1DyDO8/view.001.fogn (CRAM input).. ok
+ 64: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
- 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
+ 65: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
-.. expected failure
-
- 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
+ 67: Filter -l Library 2 (SAM input) .. ok
+ 68: Count -l Library 2 (SAM input) .. ok
-.. expected failure
+ 69: Filter -l Library 2 (BAM input) .. ok
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
+ 71: Filter -l Library 2 (CRAM input) .. ok
-.. expected failure
-
- 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
-
- 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
-
- 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
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1322,132 +1400,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 4: cat BAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 5: cat recompressed BAM files to stdout .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 6: cat CRAM files to stdout .. ok
+
+ 7: cat BAM files with new header .. ok
+
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1459,12 +1542,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/hRK7Uk3K8T - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/2wJy_SzHz1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1487,24 +1600,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1514,6 +1694,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1530,22 +1719,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- make -j6 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a
+ make -j8 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1567,16 +1755,17 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
@@ -1590,8 +1779,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1607,60 +1796,60 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/a4db01d86871ceebf61700b71d39c7d64360b6.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/a4db01d86871ceebf61700b71d39c7d64360b6.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2b/a4db01d86871ceebf61700b71d39c7d64360b6.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/875b898da27b9824c4268da1ccafdf7c74ecfc.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/875b898da27b9824c4268da1ccafdf7c74ecfc.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/875b898da27b9824c4268da1ccafdf7c74ecfc.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/2301411343eb88d2a8c512fcbe146e859ca11e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/2301411343eb88d2a8c512fcbe146e859ca11e.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c6/2301411343eb88d2a8c512fcbe146e859ca11e.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cc
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cc/f06659eadac55d4dfab9a9a27142b733c81e85.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cc/f06659eadac55d4dfab9a9a27142b733c81e85.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cc/f06659eadac55d4dfab9a9a27142b733c81e85.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/19e3e71b027598a1027046c503153cfac91a80.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/19e3e71b027598a1027046c503153cfac91a80.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/19e3e71b027598a1027046c503153cfac91a80.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/28c0c68ca14f578ed421d9fe374a84deb8cc01.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/28c0c68ca14f578ed421d9fe374a84deb8cc01.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/06/28c0c68ca14f578ed421d9fe374a84deb8cc01.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/11149395c356ea0d209051e23aef8587486df8.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/11149395c356ea0d209051e23aef8587486df8.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/11149395c356ea0d209051e23aef8587486df8.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libdl.so.2 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against ld-linux-aarch64.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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=0628c0c68ca14f578ed421d9fe374a84deb8cc01 2ba4db01d86871ceebf61700b71d39c7d64360b6 ac11149395c356ea0d209051e23aef85 [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1670,22 +1859,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_arm64.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_arm64.deb'.
+ dpkg-genchanges -B -marm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1329
+Build finished at 20160205-1630
Finished
────────
@@ -1702,108 +1891,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_arm64.changes:
+samtools_1.3-1_arm64.changes:
─────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: arm64
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
-Maintainer: arm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Maintainer: arm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- d6163cc7e664c4c9bdefa5069d0232abbbc2d88f 416002 samtools-dbgsym_1.2-4_arm64.deb
- b91ef152719eb861b128151fcb9b5ebee13529ca 349244 samtools_1.2-4_arm64.deb
+ 5bcb890c9467c769b4fa4d446e2eeff9e098c857 466886 samtools-dbgsym_1.3-1_arm64.deb
+ 55dd09f94f63a2c7a290fb3556fae1d19e0d4721 224754 samtools_1.3-1_arm64.deb
Checksums-Sha256:
- 58ac5d3ad541b490b2e1e55a6bc89418ea870129603fbe55f1dec5d8ee71a5f7 416002 samtools-dbgsym_1.2-4_arm64.deb
- c55f1142a75b3c4dd185e4a4298f23dbb68cb7ed0569012a0a2eed1868317328 349244 samtools_1.2-4_arm64.deb
+ 7a2b90814726203831c3addac0744e4cc5c0a53b8bd5556e055424d2d31e05c7 466886 samtools-dbgsym_1.3-1_arm64.deb
+ 4720931bb49f384c8f0c053a46495eed78d4c655532bc7174906e85c7f8b12ee 224754 samtools_1.3-1_arm64.deb
Files:
- 47fa75913c4cda3f9689e559c79a4549 416002 debug extra samtools-dbgsym_1.2-4_arm64.deb
- fdcd20a56bb1340bb7bd04ff7a9bf38c 349244 science optional samtools_1.2-4_arm64.deb
+ c5a0005797ff6bc6e7fea7f9c0c581d7 466886 debug extra samtools-dbgsym_1.3-1_arm64.deb
+ 9310bf86b11396e1cbf179a3ed4001db 224754 science optional samtools_1.3-1_arm64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_arm64.deb
+samtools-dbgsym_1.3-1_arm64.deb
───────────────────────────────
new debian package, version 2.0.
- size 416002 bytes: control archive=813 bytes.
+ size 466886 bytes: control archive=817 bytes.
646 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 521
- Depends: samtools (= 1.2-4)
+ Installed-Size: 552
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 0628c0c68ca14f578ed421d9fe374a84deb8cc01 2ba4db01d86871ceebf61700b71d39c7d64360b6 ac11149395c356ea0d209051e23aef8587486df8 ba875b898da27b9824c4268da1ccafdf7c74ecfc c62301411343eb88d2a8c512fcbe146e859ca11e ccf06659eadac55d4dfab9a9a27142b733c81e85 e219e3e71b027598a1027046c503153cfac91a80
+
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/06/
+-rw-r--r-- root/root 21424 2016-02-05 16:30 ./usr/lib/debug/.build-id/06/28c0c68ca14f578ed421d9fe374a84deb8cc01.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/2b/
+-rw-r--r-- root/root 22088 2016-02-05 16:30 ./usr/lib/debug/.build-id/2b/a4db01d86871ceebf61700b71d39c7d64360b6.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/ac/
+-rw-r--r-- root/root 452832 2016-02-05 16:30 ./usr/lib/debug/.build-id/ac/11149395c356ea0d209051e23aef8587486df8.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/ba/
+-rw-r--r-- root/root 10384 2016-02-05 16:30 ./usr/lib/debug/.build-id/ba/875b898da27b9824c4268da1ccafdf7c74ecfc.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/c6/
+-rw-r--r-- root/root 13000 2016-02-05 16:30 ./usr/lib/debug/.build-id/c6/2301411343eb88d2a8c512fcbe146e859ca11e.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/cc/
+-rw-r--r-- root/root 13256 2016-02-05 16:30 ./usr/lib/debug/.build-id/cc/f06659eadac55d4dfab9a9a27142b733c81e85.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/lib/debug/.build-id/e2/
+-rw-r--r-- root/root 13264 2016-02-05 16:30 ./usr/lib/debug/.build-id/e2/19e3e71b027598a1027046c503153cfac91a80.debug
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-05 16:30 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_arm64.deb
────────────────────────
new debian package, version 2.0.
- size 349244 bytes: control archive=1607 bytes.
+ size 224754 bytes: control archive=1634 bytes.
807 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 960
- Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 664
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1816,47 +2005,48 @@ samtools_1.2-4_arm64.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/bin/
+-rwxr-xr-x root/root 18608 2016-02-05 16:30 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10392 2016-02-05 16:30 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10392 2016-02-05 16:30 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10424 2016-02-05 16:30 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10352 2016-02-05 16:30 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 376920 2016-02-05 16:30 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 26888 2016-02-05 16:30 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 16:30 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 16:30 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 16:30 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 16:30 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 16:30 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1876,23 +2066,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: arm64
-Build-Space: 16068
-Build-Time: 685
+Build-Space: 16820
+Build-Time: 698
Distribution: sid
Host Architecture: arm64
-Install-Time: 17
-Job: samtools_1.2-4
-Machine Architecture: arm64
+Install-Time: 25
+Job: samtools_1.3-1
+Machine Architecture: armhf
Package: samtools
-Package-Time: 724
-Source-Version: 1.2-4
-Space: 16068
+Package-Time: 768
+Source-Version: 1.3-1
+Space: 16820
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151221-1329
-Build needed 00:12:04, 16068k disc space
-Signature with key 'FD6F04EA' requested:
- signfile /home/buildd/build/samtools_1.2-4_arm64.changes FD6F04EA
+Finished at 20160205-1630
+Build needed 00:12:48, 16820k disc space
+Signature with key 'B292CA05' requested:
+ signfile /home/buildd/build/samtools_1.3-1_arm64.changes B292CA05
Successfully signed changes file
diff --git a/armel.log b/armel.log
index 6c39805..520189f 100644
--- a/armel.log
+++ b/armel.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arnold.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on henze.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (armel) 21 Dec 2015 17:43 ║
+║ samtools 1.3-1 (armel) 05 Feb 2016 17:15 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
-Machine Architecture: armel
+Machine Architecture: armhf
Host Architecture: armel
Build Architecture: armel
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-7VO8XJ/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-7VO8XJ' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-armel-sbuild-d8a5be7c-0840-49b8-a74b-db6b5daa15ff' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror.bytemark.co.uk/debian unstable InRelease [265 kB]
-Get:2 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:1 http://ftp.uk.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [278 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)
+Get:4 http://ftp.uk.debian.org/debian unstable/main Sources [8513 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/non-free Sources [106 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main armel Packages [7878 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [181 kB]
+Get:10 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:11 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:12 http://ftp.debian.org/debian unstable/main armel Packages [7878 kB]
+Get:13 http://ftp.uk.debian.org/debian unstable/contrib armel Packages [47.1 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib armel Packages [47.1 kB]
+Get:15 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:16 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [2228 B]
+Get:17 http://incoming.debian.org/debian-buildd buildd-unstable/main armel Packages [164 kB]
+Get:18 http://incoming.debian.org/debian-buildd buildd-unstable/contrib armel Packages [1108 B]
+Fetched 34.2 MB in 17s (1964 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 25s (148 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-T8WOr9/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-k1gxXu/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
-Need to get 0 B/774 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 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-T8WOr9/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
+Get:1 file:/«BUILDDIR»/resolver-k1gxXu/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 ... 12037 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 ... 12052 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-1IfftF/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-SZvldM/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,77 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 8 not upgraded.
+Need to get 19.8 MB/19.8 MB of archives.
+After this operation, 75.5 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-SZvldM/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 http://ftp.uk.debian.org/debian unstable/main armel bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.uk.debian.org/debian unstable/main armel groff-base armel 1.22.3-7 [1108 kB]
+Get:4 http://ftp.uk.debian.org/debian unstable/main armel bsdmainutils armel 9.0.6+b1 [178 kB]
+Get:5 http://ftp.uk.debian.org/debian unstable/main armel libpipeline1 armel 1.4.1-2 [23.6 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/main armel man-db armel 2.7.5-1 [977 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/main armel autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main armel libsigsegv2 armel 2.10-4+b1 [28.6 kB]
+Get:9 http://ftp.uk.debian.org/debian unstable/main armel libunistring0 armel 0.9.3-5.2+b1 [253 kB]
+Get:10 http://ftp.uk.debian.org/debian unstable/main armel libmagic1 armel 1:5.25-2 [252 kB]
+Get:11 http://ftp.uk.debian.org/debian unstable/main armel file armel 1:5.25-2 [61.1 kB]
+Get:12 http://ftp.uk.debian.org/debian unstable/main armel gettext-base armel 0.19.7-2 [111 kB]
+Get:13 http://ftp.uk.debian.org/debian unstable/main armel libicu55 armel 55.1-7 [7340 kB]
+Get:14 http://ftp.uk.debian.org/debian unstable/main armel libxml2 armel 2.9.3+dfsg1-1 [803 kB]
+Get:15 http://ftp.uk.debian.org/debian unstable/main armel m4 armel 1.4.17-5 [239 kB]
+Get:16 http://ftp.uk.debian.org/debian unstable/main armel autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.uk.debian.org/debian unstable/main armel autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.uk.debian.org/debian unstable/main armel automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.uk.debian.org/debian unstable/main armel libffi6 armel 3.2.1-4 [18.5 kB]
+Get:20 http://ftp.uk.debian.org/debian unstable/main armel libglib2.0-0 armel 2.46.2-3 [2486 kB]
+Get:21 http://ftp.uk.debian.org/debian unstable/main armel libcroco3 armel 0.6.11-1 [132 kB]
+Get:22 http://ftp.uk.debian.org/debian unstable/main armel gettext armel 0.19.7-2 [1406 kB]
+Get:23 http://ftp.uk.debian.org/debian unstable/main armel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.uk.debian.org/debian unstable/main armel po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.uk.debian.org/debian unstable/main armel libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.uk.debian.org/debian unstable/main armel libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.uk.debian.org/debian unstable/main armel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.uk.debian.org/debian unstable/main armel dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.uk.debian.org/debian unstable/main armel debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.uk.debian.org/debian unstable/main armel libhts1 armel 1.3-1 [206 kB]
+Get:31 http://ftp.uk.debian.org/debian unstable/main armel libhts-dev armel 1.3-1 [263 kB]
+Get:32 http://ftp.uk.debian.org/debian unstable/main armel libio-pty-perl armel 1:1.08-1.1+b1 [33.2 kB]
+Get:33 http://ftp.uk.debian.org/debian unstable/main armel libtinfo-dev armel 6.0+20151024-2 [66.4 kB]
+Get:34 http://ftp.uk.debian.org/debian unstable/main armel libncurses5-dev armel 6.0+20151024-2 [158 kB]
+Get:35 http://ftp.uk.debian.org/debian unstable/main armel tabix armel 1.3-1 [194 kB]
+Get:36 http://ftp.uk.debian.org/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 17.7 MB in 1s (15.6 MB/s)
+Fetched 19.8 MB in 1s (17.1 MB/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 ... 12037 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 ... 12052 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_1.22.3-4_armel.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_armel.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_armel.deb ...
+Unpacking libpipeline1:armel (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_armel.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:armel.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_armel.deb ...
+Unpacking libsigsegv2:armel (2.10-4+b1) ...
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) ...
@@ -223,53 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_armel.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:armel.
-Preparing to unpack .../libicu55_55.1-6_armel.deb ...
-Unpacking libicu55:armel (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_armel.deb ...
+Unpacking libicu55:armel (55.1-7) ...
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 m4.
+Preparing to unpack .../archives/m4_1.4.17-5_armel.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_armel.deb ...
+Unpacking libglib2.0-0:armel (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_armel.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:armel.
-Preparing to unpack .../libhts1_1.2.1-2_armel.deb ...
-Unpacking libhts1:armel (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_armel.deb ...
+Unpacking libhts1:armel (1.3-1) ...
Selecting previously unselected package libhts-dev:armel.
-Preparing to unpack .../libhts-dev_1.2.1-2_armel.deb ...
-Unpacking libhts-dev:armel (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_armel.deb ...
+Unpacking libhts-dev:armel (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_armel.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -280,59 +306,66 @@ Selecting previously unselected package libncurses5-dev:armel.
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_1.2.1-2_armel.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../archives/tabix_1.3-1_armel.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:armel (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:armel (2.10-4+b1) ...
Setting up libunistring0:armel (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:armel (55.1-7) ...
Setting up libxml2:armel (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:armel (3.2.1-4) ...
-Setting up libglib2.0-0:armel (2.46.2-1) ...
+Setting up libglib2.0-0:armel (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armel (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:armel (1.3-1) ...
+Setting up libhts-dev:armel (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:armel (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
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_2.25.90.20151209-1 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 [...]
+Kernel: Linux 3.16.0-4-armmp-lpae armhf (armv7l)
+Toolchain package versions: binutils_2.26-3 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-3 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,36 +403,43 @@ SCHROOT_CHROOT_NAME=sid-armel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-armel-sbuild-c2aa3adc-a9a5-4aad-b663-b5ed5764a2bf
+SCHROOT_SESSION_ID=sid-armel-sbuild-d8a5be7c-0840-49b8-a74b-db6b5daa15ff
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=c11131
+XDG_SESSION_ID=1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture armel
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j4 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j4 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -422,189 +461,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=arm-linux-gnueabi --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --libexecdir=\${prefix}/lib/arm-linux-gnueabi --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/arm-linux-gnueabi/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/arm-linux-gnueabi/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/arm-linux-gnueabi/libhts.a -lhts -lcurses -lm -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
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/arm-linux-gnueabi/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test 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/glz6ctagQ_/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/Is7syFcP_X/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Is7syFcP_X/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Is7syFcP_X/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/glz6ctagQ_/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/glz6ctagQ_/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 1:100-104 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/Is7syFcP_X/dict.fa.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/glz6ctagQ_/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/glz6ctagQ_/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/Is7syFcP_X/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/glz6ctagQ_/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/Is7syFcP_X/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/Is7syFcP_X/large_chrom.bam ref2:1-541556283
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/glz6ctagQ_/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/glz6ctagQ_/mpileup.bam.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/Is7syFcP_X/mpileup.bam.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Is7syFcP_X/mpileup.bam.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/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/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/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/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/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/glz6ctagQ_/mpileup.cram.list -f /tmp/glz6ctagQ_/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/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Is7syFcP_X/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Is7syFcP_X/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -643,7 +737,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -673,7 +771,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -690,9 +796,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -724,6 +828,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -826,83 +934,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/glz6ctagQ_/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/Is7syFcP_X/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/glz6ctagQ_/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/Is7syFcP_X/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/glz6ctagQ_/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/Is7syFcP_X/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/glz6ctagQ_/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/Is7syFcP_X/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/glz6ctagQ_/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/glz6ctagQ_/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input).. ok
- 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
+ 67: Filter -l Library 2 (SAM input) .. ok
- 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
+ 68: Count -l Library 2 (SAM input) .. ok
+ 69: Filter -l Library 2 (BAM input) .. ok
-.. expected failure
-
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
- 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
+ 71: Filter -l Library 2 (CRAM input) .. ok
-
-.. expected failure
-
- 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
-
- 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
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1322,132 +1400,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
+
+ 6: cat CRAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 7: cat BAM files with new header .. ok
- 5: cat BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
+test_depad:
+ Generate BAM file .. ok
-.. expected failure
+ depad (SAM input) .. ok
- 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
+ depad -s (SAM input) .. ok
+ depad -u (SAM input) .. ok
-.. expected failure
+ depad -1 (SAM input) .. ok
- 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
+ depad (BAM input) .. ok
+ depad -s (BAM input) .. ok
-.. expected failure
+ depad -u (BAM input) .. ok
- 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
+ depad -1 (BAM input) .. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
-.. expected failure
-
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1459,12 +1542,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/XquZzCyn01 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/TLzZ0vKq6c - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1487,382 +1600,106 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
-Number of tests:
- total .. 368
- passed .. 336
- failed .. 0
- expected failure .. 32
- unexpected pass .. 0
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
-test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
-test/merge/test_rtrans_build
-test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-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}'
-
-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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/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/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}
- 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_armel.deb'.
- dpkg-deb --build debian/samtools ..
-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 20151221-1757
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
-Finished
-────────
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
-I: Built successfully
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build Chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
-samtools_1.2-4_armel.changes:
-─────────────────────────────
+ ERR:
+.. failed ...
-Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
-Source: samtools
-Binary: samtools samtools-test
-Architecture: armel
-Version: 1.2-4
-Distribution: sid
-Urgency: medium
-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: 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:
- fbf95ea98bfcb2677eacad9da0bd0c61cc714749 399216 samtools-dbgsym_1.2-4_armel.deb
- 30015490b8653c0a1493bae4617f2af57ab7e977 336704 samtools_1.2-4_armel.deb
-Checksums-Sha256:
- fef97263a917279c26ec50df9b7fc4468bbd47c11e1927580dd7496637c9f58f 399216 samtools-dbgsym_1.2-4_armel.deb
- fbe745f379bbeee72f8d9f9cab8a68e021db8dca22513fcff2af3003429b380f 336704 samtools_1.2-4_armel.deb
-Files:
- 78d6e0429bb10c10bbe8ab8c6dfb2ba7 399216 debug extra samtools-dbgsym_1.2-4_armel.deb
- 55c2dad457c9e3de2a3fbceaecb07e49 336704 science optional samtools_1.2-4_armel.deb
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
+ ERR:
+.. failed ...
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
-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 336704 bytes: control archive=1607 bytes.
- 807 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
- Package: samtools
- Version: 1.2-4
- Architecture: armel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 969
- Depends: libc6 (>= 2.15), 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 2015-12-21 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 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 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 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 2015-12-21 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 2015-12-21 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
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+
+Number of tests:
+ total .. 416
+ passed .. 396
+ failed .. 2
+ expected failure .. 18
+ unexpected pass .. 0
+
+Makefile:201: recipe for target 'test' failed
+make[2]: *** [test] Error 1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j4 test BGZIP=/usr/bin/bgzip returned exit code 2
+debian/rules:25: recipe for target 'override_dh_auto_test' failed
+make[1]: *** [override_dh_auto_test] Error 2
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+debian/rules:6: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20160205-1721
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1876,23 +1713,20 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armel
-Build-Space: 15724
-Build-Time: 720
+Build-Space: 18912
+Build-Time: 240
Distribution: sid
+Fail-Stage: build
Host Architecture: armel
-Install-Time: 39
-Job: samtools_1.2-4
-Machine Architecture: armel
+Install-Time: 35
+Job: samtools_1.3-1
+Machine Architecture: armhf
Package: samtools
-Package-Time: 801
-Source-Version: 1.2-4
-Space: 15724
-Status: successful
-Version: 1.2-4
+Package-Time: 349
+Source-Version: 1.3-1
+Space: 18912
+Status: attempted
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160205-1721
+Build needed 00:05:49, 18912k disc space
diff --git a/i386.log b/i386.log
index 885124e..66c5a52 100644
--- a/i386.log
+++ b/i386.log
@@ -1,47 +1,42 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-csail-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-grnet-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (i386) 21 Dec 2015 13:17 ║
+║ samtools 1.3-1 (i386) 05 Feb 2016 16:24 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: i386
Build Architecture: i386
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-zW6LxR/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-zW6LxR' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-6c935caa-c350-4653-bfac-a4bfadd6ca0a' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.gr.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main i386 Packages [179 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib i386 Packages [2684 B]
+Get:10 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:11 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:12 http://ftp.debian.org/debian unstable/main i386 Packages [8087 kB]
+Get:13 http://ftp.debian.org/debian unstable/contrib i386 Packages [58.7 kB]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+E: Release file for http://ftp.gr.debian.org/debian/dists/unstable/InRelease is expired (invalid since 1h 25min 39s). Updates for this repository will not be applied.
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
@@ -60,15 +55,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 1s (3705 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +77,16 @@ 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-Kx9D7o/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-8OplFR/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-8OplFR/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +101,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 18 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]
+Get:1 file:/«BUILDDIR»/resolver-8OplFR/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 ... 12351 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 ... 12366 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-rqXVAe/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-EvA3mH/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,77 +137,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 18 not upgraded.
+Need to get 21.1 MB/21.1 MB of archives.
+After this operation, 76.6 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-EvA3mH/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [992 B]
+Get:2 http://ftp.debian.org/debian unstable/main i386 bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.debian.org/debian unstable/main i386 groff-base i386 1.22.3-7 [1185 kB]
+Get:4 http://ftp.debian.org/debian unstable/main i386 bsdmainutils i386 9.0.6+b1 [183 kB]
+Get:5 http://ftp.debian.org/debian unstable/main i386 libpipeline1 i386 1.4.1-2 [29.6 kB]
+Get:6 http://ftp.debian.org/debian unstable/main i386 man-db i386 2.7.5-1 [1011 kB]
+Get:7 http://ftp.debian.org/debian unstable/main i386 autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.debian.org/debian unstable/main i386 libsigsegv2 i386 2.10-4+b1 [29.4 kB]
+Get:9 http://ftp.debian.org/debian unstable/main i386 libunistring0 i386 0.9.3-5.2+b1 [288 kB]
+Get:10 http://ftp.debian.org/debian unstable/main i386 libmagic1 i386 1:5.25-2 [261 kB]
+Get:11 http://ftp.debian.org/debian unstable/main i386 file i386 1:5.25-2 [61.5 kB]
+Get:12 http://ftp.debian.org/debian unstable/main i386 gettext-base i386 0.19.7-2 [116 kB]
+Get:13 http://ftp.debian.org/debian unstable/main i386 libicu55 i386 55.1-7 [7762 kB]
+Get:14 http://ftp.debian.org/debian unstable/main i386 libxml2 i386 2.9.3+dfsg1-1 [951 kB]
+Get:15 http://ftp.debian.org/debian unstable/main i386 m4 i386 1.4.17-5 [255 kB]
+Get:16 http://ftp.debian.org/debian unstable/main i386 autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.debian.org/debian unstable/main i386 autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.debian.org/debian unstable/main i386 automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.debian.org/debian unstable/main i386 libffi6 i386 3.2.1-4 [19.5 kB]
+Get:20 http://ftp.debian.org/debian unstable/main i386 libglib2.0-0 i386 2.46.2-3 [2707 kB]
+Get:21 http://ftp.debian.org/debian unstable/main i386 libcroco3 i386 0.6.11-1 [149 kB]
+Get:22 http://ftp.debian.org/debian unstable/main i386 gettext i386 0.19.7-2 [1481 kB]
+Get:23 http://ftp.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.debian.org/debian unstable/main i386 po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.debian.org/debian unstable/main i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.debian.org/debian unstable/main i386 debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.debian.org/debian unstable/main i386 libhts1 i386 1.3-1 [263 kB]
+Get:31 http://ftp.debian.org/debian unstable/main i386 libhts-dev i386 1.3-1 [308 kB]
+Get:32 http://ftp.debian.org/debian unstable/main i386 libio-pty-perl i386 1:1.08-1.1+b1 [33.8 kB]
+Get:33 http://ftp.debian.org/debian unstable/main i386 libtinfo-dev i386 6.0+20151024-2 [76.6 kB]
+Get:34 http://ftp.debian.org/debian unstable/main i386 libncurses5-dev i386 6.0+20151024-2 [177 kB]
+Get:35 http://ftp.debian.org/debian unstable/main i386 tabix i386 1.3-1 [247 kB]
+Get:36 http://ftp.debian.org/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 18.9 MB in 0s (42.1 MB/s)
+Fetched 21.1 MB in 1s (11.5 MB/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 ... 12351 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 12366 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_1.22.3-4_i386.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_i386.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_i386.deb ...
+Unpacking libpipeline1:i386 (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_i386.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:i386.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_i386.deb ...
+Unpacking libsigsegv2:i386 (2.10-4+b1) ...
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) ...
@@ -223,53 +232,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_i386.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:i386.
-Preparing to unpack .../libicu55_55.1-6_i386.deb ...
-Unpacking libicu55:i386 (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_i386.deb ...
+Unpacking libicu55:i386 (55.1-7) ...
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 m4.
+Preparing to unpack .../archives/m4_1.4.17-5_i386.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_i386.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:i386.
-Preparing to unpack .../libhts1_1.2.1-2_i386.deb ...
-Unpacking libhts1:i386 (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_i386.deb ...
+Unpacking libhts1:i386 (1.3-1) ...
Selecting previously unselected package libhts-dev:i386.
-Preparing to unpack .../libhts-dev_1.2.1-2_i386.deb ...
-Unpacking libhts-dev:i386 (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_i386.deb ...
+Unpacking libhts-dev:i386 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_i386.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -280,50 +301,57 @@ Selecting previously unselected package libncurses5-dev:i386.
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_1.2.1-2_i386.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../archives/tabix_1.3-1_i386.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:i386 (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:i386 (2.10-4+b1) ...
Setting up libunistring0:i386 (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:i386 (55.1-7) ...
Setting up libxml2:i386 (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:i386 (3.2.1-4) ...
-Setting up libglib2.0-0:i386 (2.46.2-1) ...
+Setting up libglib2.0-0:i386 (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:i386 (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:i386 (1.3-1) ...
+Setting up libhts-dev:i386 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -331,8 +359,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-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+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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.24-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +371,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,36 +398,43 @@ SCHROOT_CHROOT_NAME=sid-i386-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-i386-sbuild-15d4cef1-a50f-494f-91b6-346ddafe30b1
+SCHROOT_SESSION_ID=sid-i386-sbuild-6c935caa-c350-4653-bfac-a4bfadd6ca0a
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=1
+XDG_SESSION_ID=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture i386
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j4 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j4 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -422,189 +456,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=i586-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/i386-linux-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-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/i386-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-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/i386-linux-gnu/libhts.a -lhts -lcurses -lm -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
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/i386-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test 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/8wT_XD_FtD/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/kLkF7CJo2N/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/8wT_XD_FtD/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/kLkF7CJo2N/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/8wT_XD_FtD/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/kLkF7CJo2N/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/8wT_XD_FtD/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/kLkF7CJo2N/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/8wT_XD_FtD/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/kLkF7CJo2N/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/8wT_XD_FtD/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/kLkF7CJo2N/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/8wT_XD_FtD/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/kLkF7CJo2N/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/8wT_XD_FtD/mpileup.bam.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/kLkF7CJo2N/mpileup.bam.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/kLkF7CJo2N/mpileup.bam.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/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/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/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/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/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/8wT_XD_FtD/mpileup.cram.list -f /tmp/8wT_XD_FtD/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/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kLkF7CJo2N/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:1050-1060 /tmp/kLkF7CJo2N/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -643,7 +732,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -673,7 +766,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -690,9 +791,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -724,6 +823,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -826,83 +929,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input) .. ok
+ 49: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input) .. ok
- 55: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (SAM input).. ok
+ 50: Count -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input) .. ok
- 56: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (SAM input).. ok
+ 51: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input) .. ok
- 57: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (BAM input).. ok
+ 52: Count -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input) .. ok
- 58: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (BAM input).. ok
+ 53: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input) .. ok
- 59: Filter -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (CRAM input).. ok
+ 54: Count -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input) .. ok
- 60: Count -R /tmp/8wT_XD_FtD/view.001.fogn -r grp2 (CRAM input).. ok
+ 55: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (SAM input).. ok
- 61: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input).. ok
+ 56: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (SAM input).. ok
- 62: Count -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (SAM input).. ok
+ 57: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (BAM input).. ok
- 63: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input).. ok
+ 58: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (BAM input).. ok
- 64: Count -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (BAM input).. ok
+ 59: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (CRAM input).. ok
- 65: Filter -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input).. ok
+ 60: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/8wT_XD_FtD/view.001.fogn (CRAM input).. ok
+ 61: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input).. ok
- 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
+ 62: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input).. ok
+ 63: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
-
+ 64: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
+ 65: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input).. ok
-.. expected failure
+ 67: Filter -l Library 2 (SAM input) .. ok
- 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
+ 68: Count -l Library 2 (SAM input) .. ok
+ 69: Filter -l Library 2 (BAM input) .. ok
-.. expected failure
-
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
- 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
+ 71: Filter -l Library 2 (CRAM input) .. ok
-
-.. expected failure
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1322,132 +1395,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 6: cat CRAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 7: cat BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1459,12 +1537,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/dCWbBNXYIG - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/pFNRNGx9cU - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1487,24 +1595,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1514,6 +1689,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1530,22 +1714,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/i386-linux-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1567,16 +1750,17 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
@@ -1590,8 +1774,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1607,59 +1791,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/4875235a42965919ba53e934390b9b0d541b44.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/4875235a42965919ba53e934390b9b0d541b44.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/4875235a42965919ba53e934390b9b0d541b44.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/42f43b3f31d06c07d8188e77384e2aa50341ec.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/42f43b3f31d06c07d8188e77384e2aa50341ec.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/42f43b3f31d06c07d8188e77384e2aa50341ec.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/7343704742e51f96ff6837d6ed9f122f407f5e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/7343704742e51f96ff6837d6ed9f122f407f5e.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/63/7343704742e51f96ff6837d6ed9f122f407f5e.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/c71dca81aa37ae5e61d59c8384466f7aa89e5b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/c71dca81aa37ae5e61d59c8384466f7aa89e5b.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/c71dca81aa37ae5e61d59c8384466f7aa89e5b.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/4dce72875dcadd1dc36f525546c674e9c91b54.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/4dce72875dcadd1dc36f525546c674e9c91b54.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/4dce72875dcadd1dc36f525546c674e9c91b54.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/f41b3def3732aff6c427e48635cc85eec92623.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/f41b3def3732aff6c427e48635cc85eec92623.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/80/f41b3def3732aff6c427e48635cc85eec92623.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/ded11e29249f2237075913304f8f436c6f31eb.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/ded11e29249f2237075913304f8f436c6f31eb.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/ded11e29249f2237075913304f8f436c6f31eb.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long were not linked against libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=08ded11e29249f2237075913304f8f436c6f31eb 637343704742e51f96ff6837d6ed9f122f407f5e 72c71dca81aa37ae5e61d59c8384466f [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1669,22 +1853,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_i386.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_i386.deb'.
+ dpkg-genchanges -B -mamd64 / i386 Build Daemon (x86-grnet-01) <buildd_amd64-x86-grnet-01 at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1319
+Build finished at 20160205-1626
Finished
────────
@@ -1701,108 +1885,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_i386.changes:
+samtools_1.3-1_i386.changes:
────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: i386
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
-Maintainer: amd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Maintainer: amd64 / i386 Build Daemon (x86-grnet-01) <buildd_amd64-x86-grnet-01 at buildd.debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- b9e0db8ff6f869b5a76124828c98f6cafe12873d 383882 samtools-dbgsym_1.2-4_i386.deb
- 97389cb22465c9f9bacb6353c4733caefe4bf43e 408656 samtools_1.2-4_i386.deb
+ 39eb05a2533e6779f2a0e688b1bf2c675b863281 425484 samtools-dbgsym_1.3-1_i386.deb
+ a5bb2525c1c8fe6db8075dda90463d0e3f1c72c1 253866 samtools_1.3-1_i386.deb
Checksums-Sha256:
- dee644872fb7f6f12330686e17492f8e7648a0891900228c20c5e030008ebaef 383882 samtools-dbgsym_1.2-4_i386.deb
- 6ebb72cf1f431bc269a84dc63ce7734bfcfbe6ca56984c2f6976ecb5cef8863b 408656 samtools_1.2-4_i386.deb
+ 9cff43d925cedb099518365844dbc629cf143eaf2ff0b5ad1e0dcb4b8dc3ada4 425484 samtools-dbgsym_1.3-1_i386.deb
+ fc7bb592cfe63039f4f9e39138ce35d77c68172f5e02ff86ec5f2f20212a7855 253866 samtools_1.3-1_i386.deb
Files:
- c2f9e4e188f35d3b5216d0dd3687e57b 383882 debug extra samtools-dbgsym_1.2-4_i386.deb
- 9c55bf0a21fd7966757c30b57db5b147 408656 science optional samtools_1.2-4_i386.deb
+ 11722047d3a93c05cf27a36824f7ebf3 425484 debug extra samtools-dbgsym_1.3-1_i386.deb
+ e2a906a2cb7feceb94193290147ec437 253866 science optional samtools_1.3-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_i386.deb
+samtools-dbgsym_1.3-1_i386.deb
──────────────────────────────
new debian package, version 2.0.
- size 383882 bytes: control archive=813 bytes.
+ size 425484 bytes: control archive=815 bytes.
645 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 450
- Depends: samtools (= 1.2-4)
+ Installed-Size: 480
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 08ded11e29249f2237075913304f8f436c6f31eb 637343704742e51f96ff6837d6ed9f122f407f5e 72c71dca81aa37ae5e61d59c8384466f7aa89e5b 80f41b3def3732aff6c427e48635cc85eec92623 a64875235a42965919ba53e934390b9b0d541b44 ac4dce72875dcadd1dc36f525546c674e9c91b54 cd42f43b3f31d06c07d8188e77384e2aa50341ec
+
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/08/
+-rw-r--r-- root/root 401104 2016-02-05 16:26 ./usr/lib/debug/.build-id/08/ded11e29249f2237075913304f8f436c6f31eb.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/63/
+-rw-r--r-- root/root 9592 2016-02-05 16:26 ./usr/lib/debug/.build-id/63/7343704742e51f96ff6837d6ed9f122f407f5e.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/72/
+-rw-r--r-- root/root 9460 2016-02-05 16:26 ./usr/lib/debug/.build-id/72/c71dca81aa37ae5e61d59c8384466f7aa89e5b.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/80/
+-rw-r--r-- root/root 18160 2016-02-05 16:26 ./usr/lib/debug/.build-id/80/f41b3def3732aff6c427e48635cc85eec92623.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/a6/
+-rw-r--r-- root/root 16928 2016-02-05 16:26 ./usr/lib/debug/.build-id/a6/4875235a42965919ba53e934390b9b0d541b44.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/ac/
+-rw-r--r-- root/root 9472 2016-02-05 16:26 ./usr/lib/debug/.build-id/ac/4dce72875dcadd1dc36f525546c674e9c91b54.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/lib/debug/.build-id/cd/
+-rw-r--r-- root/root 7088 2016-02-05 16:26 ./usr/lib/debug/.build-id/cd/42f43b3f31d06c07d8188e77384e2aa50341ec.debug
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-05 16:26 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_i386.deb
───────────────────────
new debian package, version 2.0.
- size 408656 bytes: control archive=1604 bytes.
- 807 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ size 253866 bytes: control archive=1629 bytes.
+ 805 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1113
- Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 720
+ Depends: libc6 (>= 2.7), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1815,47 +1999,48 @@ samtools_1.2-4_i386.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/bin/
+-rwxr-xr-x root/root 17956 2016-02-05 16:26 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9748 2016-02-05 16:26 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2016-02-05 16:26 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9768 2016-02-05 16:26 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5636 2016-02-05 16:26 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 449092 2016-02-05 16:26 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22116 2016-02-05 16:26 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 16:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 16:26 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 16:26 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 16:26 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 16:26 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1875,23 +2060,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: i386
-Build-Space: 15936
-Build-Time: 86
+Build-Space: 16388
+Build-Time: 78
Distribution: sid
Host Architecture: i386
Install-Time: 13
-Job: samtools_1.2-4
+Job: samtools_1.3-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 118
-Source-Version: 1.2-4
-Space: 15936
+Package-Time: 105
+Source-Version: 1.3-1
+Space: 16388
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160205-1626
+Build needed 00:01:45, 16388k disc space
+Signature with key '94DCC119' requested:
+ signfile /home/buildd/build/samtools_1.3-1_i386.changes 94DCC119
Successfully signed changes file
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index b9a9472..c8dddf0 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -2,44 +2,44 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fayrfax.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (kfreebsd-amd64) 21 Dec 2015 13:17 ║
+║ samtools 1.3-1 (kfreebsd-amd64) 05 Feb 2016 16:25 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: kfreebsd-amd64
Host Architecture: kfreebsd-amd64
Build Architecture: kfreebsd-amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-NvGimM/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-NvGimM' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-a-sbuild-1454689512-17467' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
-Get:2 http://ftp.de.debian.org/debian unstable InRelease [265 kB]
+Get:1 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://ftp.de.debian.org/debian unstable InRelease [278 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)
+Get:4 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-amd64 Packages [134 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-amd64 Packages [32 B]
+Get:10 http://ftp.de.debian.org/debian unstable/main Sources [8513 kB]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-amd64 Packages [7415 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [44.3 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [106 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 Packages [7415 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [44.3 kB]
+Fetched 33.3 MB in 8s (3740 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 0s (6295 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-d0e_ot/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ySPn1z/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-ySPn1z/apt_archive ./ Packages [532 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 6 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]
+Get:1 file:/«BUILDDIR»/resolver-ySPn1z/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 ... 12027 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 ... 12046 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-9ii9Cr/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-WxHOwm/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ Packages [750 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,83 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 6 not upgraded.
+Need to get 20.6 MB/20.6 MB of archives.
+After this operation, 76.0 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-WxHOwm/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [994 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:3 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 groff-base kfreebsd-amd64 1.22.3-7 [1075 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:5 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libpipeline1 kfreebsd-amd64 1.4.1-2 [27.7 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:7 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libsigsegv2 kfreebsd-amd64 2.10-4+b1 [28.1 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:12 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 gettext-base kfreebsd-amd64 0.19.7-2 [115 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libicu55 kfreebsd-amd64 55.1-7 [7648 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]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 m4 kfreebsd-amd64 1.4.17-5 [255 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libffi6 kfreebsd-amd64 3.2.1-4 [19.8 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libglib2.0-0 kfreebsd-amd64 2.46.2-3 [2635 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libcroco3 kfreebsd-amd64 0.6.11-1 [143 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 gettext kfreebsd-amd64 0.19.7-2 [1475 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts1 kfreebsd-amd64 1.3-1 [246 kB]
+Get:31 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts-dev kfreebsd-amd64 1.3-1 [302 kB]
+Get:32 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:33 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtinfo-dev kfreebsd-amd64 6.0+20151024-2 [77.4 kB]
+Get:34 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libncurses5-dev kfreebsd-amd64 6.0+20151024-2 [174 kB]
+Get:35 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 tabix kfreebsd-amd64 1.3-1 [239 kB]
+Get:36 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 18.2 MB in 2s (6898 kB/s)
+Fetched 20.6 MB in 2s (9300 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 12027 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 100%
(Reading database ... 12046 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_1.22.3-4_kfreebsd-amd64.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_kfreebsd-amd64.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_kfreebsd-amd64.deb ...
+Unpacking libpipeline1:kfreebsd-amd64 (1.4.1-2) ...
Selecting previously unselected package man-db.
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_3.2.1-4_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 autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:kfreebsd-amd64.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_kfreebsd-amd64.deb ...
+Unpacking libsigsegv2:kfreebsd-amd64 (2.10-4+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) ...
@@ -229,47 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_kfreebsd-amd64.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:kfreebsd-amd64.
-Preparing to unpack .../libicu55_55.1-6_kfreebsd-amd64.deb ...
-Unpacking libicu55:kfreebsd-amd64 (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_kfreebsd-amd64.deb ...
+Unpacking libicu55:kfreebsd-amd64 (55.1-7) ...
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 m4.
+Preparing to unpack .../m4_1.4.17-5_kfreebsd-amd64.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
+Selecting previously unselected package libffi6:kfreebsd-amd64.
+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_2.46.2-3_kfreebsd-amd64.deb ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_kfreebsd-amd64.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:kfreebsd-amd64.
-Preparing to unpack .../libhts1_1.2.1-2_kfreebsd-amd64.deb ...
-Unpacking libhts1:kfreebsd-amd64 (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_kfreebsd-amd64.deb ...
+Unpacking libhts1:kfreebsd-amd64 (1.3-1) ...
Selecting previously unselected package libhts-dev:kfreebsd-amd64.
-Preparing to unpack .../libhts-dev_1.2.1-2_kfreebsd-amd64.deb ...
-Unpacking libhts-dev:kfreebsd-amd64 (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_kfreebsd-amd64.deb ...
+Unpacking libhts-dev:kfreebsd-amd64 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
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) ...
@@ -280,50 +306,57 @@ Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
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_1.2.1-2_kfreebsd-amd64.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../tabix_1.3-1_kfreebsd-amd64.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:kfreebsd-amd64 (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: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 autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:kfreebsd-amd64 (2.10-4+b1) ...
Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:kfreebsd-amd64 (55.1-7) ...
Setting up libxml2:kfreebsd-amd64 (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up libffi6:kfreebsd-amd64 (3.2.1-4) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.46.2-3) ...
+No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-amd64 (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:kfreebsd-amd64 (1.3-1) ...
+Setting up libhts-dev:kfreebsd-amd64 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -331,8 +364,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: GNU/kFreeBSD 10.1-0-amd64 kfreebsd-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 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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,35 +403,41 @@ SCHROOT_CHROOT_NAME=sid-k-a-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-k-a-sbuild-1450703851-16756
+SCHROOT_SESSION_ID=sid-k-a-sbuild-1454689512-17467
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-USERNAME=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture kfreebsd-amd64
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j2 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j2 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -421,189 +459,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=x86_64-kfreebsd-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-kfreebsd-gnu --libexecdir=\${prefix}/lib/x86_64-kfreebsd-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j2 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-kfreebsd-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/x86_64-kfreebsd-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/x86_64-kfreebsd-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/x86_64-kfreebsd-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/x86_64-kfreebsd-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/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-kfreebsd-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/x86_64-kfreebsd-gnu/libhts.a -lhts -lcurses -lm -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
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-kfreebsd-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j2 test 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/aHQAAjFh4l/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/9n3LVwBXro/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/9n3LVwBXro/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/9n3LVwBXro/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/aHQAAjFh4l/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/aHQAAjFh4l/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/aHQAAjFh4l/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/9n3LVwBXro/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/aHQAAjFh4l/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/9n3LVwBXro/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/aHQAAjFh4l/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/9n3LVwBXro/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/9n3LVwBXro/large_chrom.bam ref2:1-541556283
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/aHQAAjFh4l/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/aHQAAjFh4l/mpileup.bam.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/9n3LVwBXro/mpileup.bam.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9n3LVwBXro/mpileup.bam.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/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/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/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/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/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/aHQAAjFh4l/mpileup.cram.list -f /tmp/aHQAAjFh4l/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/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9n3LVwBXro/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9n3LVwBXro/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -642,7 +735,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -672,7 +769,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -689,9 +794,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -723,6 +826,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -825,83 +932,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input) .. ok
-
- 55: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (SAM input).. ok
-
- 56: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (SAM input).. ok
+ 49: Filter -R /tmp/9n3LVwBXro/view.001.fogn (SAM input) .. ok
- 57: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (BAM input).. ok
+ 50: Count -R /tmp/9n3LVwBXro/view.001.fogn (SAM input) .. ok
- 58: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (BAM input).. ok
+ 51: Filter -R /tmp/9n3LVwBXro/view.001.fogn (BAM input) .. ok
- 59: Filter -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (CRAM input).. ok
+ 52: Count -R /tmp/9n3LVwBXro/view.001.fogn (BAM input) .. ok
- 60: Count -R /tmp/aHQAAjFh4l/view.001.fogn -r grp2 (CRAM input).. ok
+ 53: Filter -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input) .. ok
- 61: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input).. ok
+ 54: Count -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input) .. ok
- 62: Count -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (SAM input).. ok
+ 55: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input).. ok
+ 56: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (SAM input).. ok
- 64: Count -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (BAM input).. ok
+ 57: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input).. ok
+ 58: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (BAM input).. ok
- 66: Count -r grp2 -R /tmp/aHQAAjFh4l/view.001.fogn (CRAM input).. ok
+ 59: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (CRAM input).. ok
- 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
+ 60: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (CRAM input).. ok
+ 61: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (SAM input).. ok
-.. expected failure
-
- 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
-
+ 62: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (SAM input).. ok
-.. expected failure
+ 63: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (BAM input).. ok
- 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
+ 64: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (BAM input).. ok
+ 65: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input).. ok
-.. expected failure
+ 66: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input).. ok
- 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
+ 67: Filter -l Library 2 (SAM input) .. ok
+ 68: Count -l Library 2 (SAM input) .. ok
-.. expected failure
+ 69: Filter -l Library 2 (BAM input) .. ok
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
+ 71: Filter -l Library 2 (CRAM input) .. ok
-.. expected failure
-
- 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
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1321,132 +1398,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 6: cat CRAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 7: cat BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1458,12 +1540,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/QNepMGrILs - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/jHQjuAIqo4 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1486,24 +1598,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1513,6 +1692,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1529,22 +1717,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
+ make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1566,19 +1753,20 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
dh_installman -a -O--parallel
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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.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
@@ -1589,8 +1777,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1606,59 +1794,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6c
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6c/a0dcdffed66e04bebefe780c7da55b92d88aa8.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6c/a0dcdffed66e04bebefe780c7da55b92d88aa8.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6c/a0dcdffed66e04bebefe780c7da55b92d88aa8.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/c66641ef64a9ab1b67330247f2fc7f880dedf0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/c66641ef64a9ab1b67330247f2fc7f880dedf0.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/c66641ef64a9ab1b67330247f2fc7f880dedf0.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/031e496d226644ffad1e26c0e3b75650cfb721.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/031e496d226644ffad1e26c0e3b75650cfb721.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/031e496d226644ffad1e26c0e3b75650cfb721.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8/f6a32d4506cc3d3971d773f1a55a3d575b6d00.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8/f6a32d4506cc3d3971d773f1a55a3d575b6d00.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8/f6a32d4506cc3d3971d773f1a55a3d575b6d00.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/dfa229c2a56fd431d411666f8d987c59418a6e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/dfa229c2a56fd431d411666f8d987c59418a6e.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ba/dfa229c2a56fd431d411666f8d987c59418a6e.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dd
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dd/30599df2868b9725e8b8b5c99d6daf3bb742b5.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dd/30599df2868b9725e8b8b5c99d6daf3bb742b5.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dd/30599df2868b9725e8b8b5c99d6daf3bb742b5.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/ffb4328e7791d91606a2eb1c8fe2834de9f8e0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/ffb4328e7791d91606a2eb1c8fe2834de9f8e0.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a5/ffb4328e7791d91606a2eb1c8fe2834de9f8e0.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools 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/maq2sam-short were not linked against libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=58031e496d226644ffad1e26c0e3b75650cfb721 65c66641ef64a9ab1b67330247f2fc7f880dedf0 6ca0dcdffed66e04bebefe780c7da55b [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1668,22 +1856,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_kfreebsd-amd64.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1319
+Build finished at 20160205-1627
Finished
────────
@@ -1700,108 +1888,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_kfreebsd-amd64.changes:
+samtools_1.3-1_kfreebsd-amd64.changes:
──────────────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-amd64
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- 906cb5118c87f18d8352bafb88f27e3587dea807 416274 samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
- 302eca107188c6e20432af89d93d5f845c3df4ff 395900 samtools_1.2-4_kfreebsd-amd64.deb
+ 030b9b39ccbb56882439cd2a7e3588c7ef228567 467494 samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
+ 410d3edf1469334f8f73379745d702bcd465050c 246338 samtools_1.3-1_kfreebsd-amd64.deb
Checksums-Sha256:
- bdaebd1039c93e96bc70ca2a5a30748c23d8172bcaa76d15ba478219b7c7fb54 416274 samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
- 299fc1830ee4795be104f1d57fcee93a1daf2a79aac488461dd7472cc23e4f96 395900 samtools_1.2-4_kfreebsd-amd64.deb
+ db209a46c20bb0a891c13e08992b902314c59dfe316f6a1b6fff13c3a528bd7c 467494 samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
+ 0d354dca18a2f907511417df8b26c24c1ed2e9a25605e300b86d946c4feff025 246338 samtools_1.3-1_kfreebsd-amd64.deb
Files:
- 1df8aadd1de5b703d97983aae5f702fe 416274 debug extra samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
- 544eccdf94e78f7cac3e399617e09950 395900 science optional samtools_1.2-4_kfreebsd-amd64.deb
+ efa5fa6a7d396c1fa136506bf0457dbe 467494 debug extra samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
+ 63568b84eb45bf598522db79167b664b 246338 science optional samtools_1.3-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_kfreebsd-amd64.deb
+samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
────────────────────────────────────────
new debian package, version 2.0.
- size 416274 bytes: control archive=821 bytes.
+ size 467494 bytes: control archive=817 bytes.
655 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 506
- Depends: samtools (= 1.2-4)
+ Installed-Size: 539
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 58031e496d226644ffad1e26c0e3b75650cfb721 65c66641ef64a9ab1b67330247f2fc7f880dedf0 6ca0dcdffed66e04bebefe780c7da55b92d88aa8 a5ffb4328e7791d91606a2eb1c8fe2834de9f8e0 badfa229c2a56fd431d411666f8d987c59418a6e dd30599df2868b9725e8b8b5c99d6daf3bb742b5 e8f6a32d4506cc3d3971d773f1a55a3d575b6d00
+
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/58/
+-rw-r--r-- root/root 11832 2016-02-05 16:27 ./usr/lib/debug/.build-id/58/031e496d226644ffad1e26c0e3b75650cfb721.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/65/
+-rw-r--r-- root/root 20808 2016-02-05 16:27 ./usr/lib/debug/.build-id/65/c66641ef64a9ab1b67330247f2fc7f880dedf0.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/6c/
+-rw-r--r-- root/root 447024 2016-02-05 16:27 ./usr/lib/debug/.build-id/6c/a0dcdffed66e04bebefe780c7da55b92d88aa8.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/a5/
+-rw-r--r-- root/root 19888 2016-02-05 16:27 ./usr/lib/debug/.build-id/a5/ffb4328e7791d91606a2eb1c8fe2834de9f8e0.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/ba/
+-rw-r--r-- root/root 11832 2016-02-05 16:27 ./usr/lib/debug/.build-id/ba/dfa229c2a56fd431d411666f8d987c59418a6e.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/dd/
+-rw-r--r-- root/root 9144 2016-02-05 16:27 ./usr/lib/debug/.build-id/dd/30599df2868b9725e8b8b5c99d6daf3bb742b5.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/lib/debug/.build-id/e8/
+-rw-r--r-- root/root 11824 2016-02-05 16:27 ./usr/lib/debug/.build-id/e8/f6a32d4506cc3d3971d773f1a55a3d575b6d00.debug
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2016-02-05 16:27 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_kfreebsd-amd64.deb
─────────────────────────────────
new debian package, version 2.0.
- size 395900 bytes: control archive=1616 bytes.
- 822 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ size 246338 bytes: control archive=1646 bytes.
+ 821 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1068
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 704
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1814,47 +2002,48 @@ samtools_1.2-4_kfreebsd-amd64.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/bin/
+-rwxr-xr-x root/root 22856 2016-02-05 16:27 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10536 2016-02-05 16:27 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10536 2016-02-05 16:27 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10576 2016-02-05 16:27 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10504 2016-02-05 16:27 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 418080 2016-02-05 16:27 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22944 2016-02-05 16:27 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 16:27 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 16:27 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 16:27 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 16:27 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 16:27 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1874,23 +2063,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-amd64
-Build-Space: 16920
-Build-Time: 87
+Build-Space: 17552
+Build-Time: 91
Distribution: sid
Host Architecture: kfreebsd-amd64
-Install-Time: 15
-Job: samtools_1.2-4
+Install-Time: 14
+Job: samtools_1.3-1
Machine Architecture: kfreebsd-amd64
Package: samtools
-Package-Time: 128
-Source-Version: 1.2-4
-Space: 16920
+Package-Time: 133
+Source-Version: 1.3-1
+Space: 17552
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151221-1319
-Build needed 00:02:08, 16920k disc space
+Finished at 20160205-1627
+Build needed 00:02:13, 17552k disc space
Signature with key '214E2A08' requested:
- signfile /home/buildd/build/samtools_1.2-4_kfreebsd-amd64.changes 214E2A08
+ signfile /home/buildd/build/samtools_1.3-1_kfreebsd-amd64.changes 214E2A08
Successfully signed changes file
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index f0bd803..668ca87 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -2,44 +2,44 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fils.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (kfreebsd-i386) 21 Dec 2015 13:20 ║
+║ samtools 1.3-1 (kfreebsd-i386) 05 Feb 2016 16:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: kfreebsd-i386
Host Architecture: kfreebsd-i386
Build Architecture: kfreebsd-i386
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-DlzCoE/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-DlzCoE' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-i-sbuild-1454689362-28265' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
+Get:1 http://ftp.debian.org/debian unstable InRelease [278 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)
+Get:3 http://ftp.de.debian.org/debian unstable InRelease [278 kB]
+Get:4 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-i386 Packages [137 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-i386 Packages [32 B]
+Get:10 http://ftp.de.debian.org/debian unstable/main Sources [8513 kB]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-i386 Packages [7403 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-i386 Packages [44.3 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [106 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 Packages [7403 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-i386 Packages [44.3 kB]
+Fetched 33.2 MB in 11s (2916 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 0s (6932 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-663JgF/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-w6zXKN/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ Packages [533 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/776 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 6 not upgraded.
+Need to get 0 B/778 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]
+Get:1 file:/«BUILDDIR»/resolver-w6zXKN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 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 ... 11668 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 ... 11687 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-dtQOBh/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-XZCsVp/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ Packages [750 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,83 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 6 not upgraded.
+Need to get 20.9 MB/20.9 MB of archives.
+After this operation, 76.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-XZCsVp/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [996 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:3 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 groff-base kfreebsd-i386 1.22.3-7 [1099 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:5 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libpipeline1 kfreebsd-i386 1.4.1-2 [29.6 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:7 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsigsegv2 kfreebsd-i386 2.10-4+b1 [28.2 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:12 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext-base kfreebsd-i386 0.19.7-2 [116 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libicu55 kfreebsd-i386 55.1-7 [7757 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]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 m4 kfreebsd-i386 1.4.17-5 [255 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libffi6 kfreebsd-i386 3.2.1-4 [18.8 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libglib2.0-0 kfreebsd-i386 2.46.2-3 [2701 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcroco3 kfreebsd-i386 0.6.11-1 [149 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext kfreebsd-i386 0.19.7-2 [1480 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts1 kfreebsd-i386 1.3-1 [263 kB]
+Get:31 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts-dev kfreebsd-i386 1.3-1 [308 kB]
+Get:32 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:33 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtinfo-dev kfreebsd-i386 6.0+20151024-2 [76.3 kB]
+Get:34 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libncurses5-dev kfreebsd-i386 6.0+20151024-2 [176 kB]
+Get:35 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 tabix kfreebsd-i386 1.3-1 [248 kB]
+Get:36 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 18.5 MB in 1s (12.3 MB/s)
+Fetched 20.9 MB in 1s (12.6 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11668 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%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11687 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_1.22.3-4_kfreebsd-i386.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_kfreebsd-i386.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_kfreebsd-i386.deb ...
+Unpacking libpipeline1:kfreebsd-i386 (1.4.1-2) ...
Selecting previously unselected package man-db.
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_3.2.1-4_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 autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:kfreebsd-i386.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_kfreebsd-i386.deb ...
+Unpacking libsigsegv2:kfreebsd-i386 (2.10-4+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) ...
@@ -229,47 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_kfreebsd-i386.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:kfreebsd-i386.
-Preparing to unpack .../libicu55_55.1-6_kfreebsd-i386.deb ...
-Unpacking libicu55:kfreebsd-i386 (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_kfreebsd-i386.deb ...
+Unpacking libicu55:kfreebsd-i386 (55.1-7) ...
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 m4.
+Preparing to unpack .../m4_1.4.17-5_kfreebsd-i386.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
+Selecting previously unselected package libffi6:kfreebsd-i386.
+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_2.46.2-3_kfreebsd-i386.deb ...
+Unpacking libglib2.0-0:kfreebsd-i386 (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_kfreebsd-i386.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:kfreebsd-i386.
-Preparing to unpack .../libhts1_1.2.1-2_kfreebsd-i386.deb ...
-Unpacking libhts1:kfreebsd-i386 (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_kfreebsd-i386.deb ...
+Unpacking libhts1:kfreebsd-i386 (1.3-1) ...
Selecting previously unselected package libhts-dev:kfreebsd-i386.
-Preparing to unpack .../libhts-dev_1.2.1-2_kfreebsd-i386.deb ...
-Unpacking libhts-dev:kfreebsd-i386 (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
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) ...
@@ -280,50 +306,57 @@ Selecting previously unselected package libncurses5-dev:kfreebsd-i386.
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_1.2.1-2_kfreebsd-i386.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../tabix_1.3-1_kfreebsd-i386.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:kfreebsd-i386 (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: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 autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:kfreebsd-i386 (2.10-4+b1) ...
Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:kfreebsd-i386 (55.1-7) ...
Setting up libxml2:kfreebsd-i386 (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up libffi6:kfreebsd-i386 (3.2.1-4) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.46.2-3) ...
+No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-i386 (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:kfreebsd-i386 (1.3-1) ...
+Setting up libhts-dev:kfreebsd-i386 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -331,8 +364,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: GNU/kFreeBSD 10.1-0-686 kfreebsd-i386 (i386)
-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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,7 +403,7 @@ SCHROOT_CHROOT_NAME=sid-k-i-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-k-i-sbuild-1450704051-17953
+SCHROOT_SESSION_ID=sid-k-i-sbuild-1454689362-28265
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -381,24 +413,31 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture kfreebsd-i386
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j2 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j2 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -420,189 +459,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=i586-kfreebsd-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-kfreebsd-gnu --libexecdir=\${prefix}/lib/i386-kfreebsd-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j2 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/i386-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/i386-kfreebsd-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/i386-kfreebsd-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/i386-kfreebsd-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/i386-kfreebsd-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/i386-kfreebsd-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/i386-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-kfreebsd-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/i386-kfreebsd-gnu/libhts.a -lhts -lcurses -lm -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
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/i386-kfreebsd-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j2 test 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/lAKSxc6s5Q/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/lPPNrK5b5B/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lPPNrK5b5B/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lPPNrK5b5B/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lAKSxc6s5Q/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lAKSxc6s5Q/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lAKSxc6s5Q/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/lPPNrK5b5B/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/lAKSxc6s5Q/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/lPPNrK5b5B/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/lAKSxc6s5Q/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/lPPNrK5b5B/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/lPPNrK5b5B/large_chrom.bam ref2:1-541556283
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/lAKSxc6s5Q/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/lAKSxc6s5Q/mpileup.bam.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/lPPNrK5b5B/mpileup.bam.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/lPPNrK5b5B/mpileup.bam.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/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/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/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/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/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/lAKSxc6s5Q/mpileup.cram.list -f /tmp/lAKSxc6s5Q/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/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lPPNrK5b5B/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:1050-1060 /tmp/lPPNrK5b5B/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -641,7 +735,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -671,7 +769,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -688,9 +794,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -722,6 +826,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -824,83 +932,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input) .. ok
-
- 55: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (SAM input).. ok
-
- 56: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (SAM input).. ok
+ 49: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input) .. ok
- 57: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (BAM input).. ok
+ 50: Count -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input) .. ok
- 58: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (BAM input).. ok
+ 51: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input) .. ok
- 59: Filter -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (CRAM input).. ok
+ 52: Count -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input) .. ok
- 60: Count -R /tmp/lAKSxc6s5Q/view.001.fogn -r grp2 (CRAM input).. ok
+ 53: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input) .. ok
- 61: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input).. ok
+ 54: Count -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input) .. ok
- 62: Count -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (SAM input).. ok
+ 55: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input).. ok
+ 56: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (SAM input).. ok
- 64: Count -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (BAM input).. ok
+ 57: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input).. ok
+ 58: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (BAM input).. ok
- 66: Count -r grp2 -R /tmp/lAKSxc6s5Q/view.001.fogn (CRAM input).. ok
+ 59: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (CRAM input).. ok
- 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
+ 60: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (CRAM input).. ok
+ 61: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input).. ok
-.. expected failure
-
- 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
-
+ 62: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input).. ok
-.. expected failure
+ 63: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input).. ok
- 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
+ 64: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input).. ok
+ 65: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input).. ok
-.. expected failure
+ 66: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input).. ok
- 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
+ 67: Filter -l Library 2 (SAM input) .. ok
+ 68: Count -l Library 2 (SAM input) .. ok
-.. expected failure
+ 69: Filter -l Library 2 (BAM input) .. ok
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
+ 71: Filter -l Library 2 (CRAM input) .. ok
-.. expected failure
-
- 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
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1320,132 +1398,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 6: cat CRAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 7: cat BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1457,12 +1540,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/OXlcZpyWfC - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/COjVupKv2E - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1485,24 +1598,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1512,6 +1692,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1528,22 +1717,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a
+ make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1565,19 +1753,20 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
dh_installman -a -O--parallel
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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.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
@@ -1588,8 +1777,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1605,59 +1794,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/9d8cdba827e4819d5fbf4ab59fe2cf4eead3f5.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/9d8cdba827e4819d5fbf4ab59fe2cf4eead3f5.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/48/9d8cdba827e4819d5fbf4ab59fe2cf4eead3f5.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f4
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f4/ac1cb650b907590b42e3a2d5f595c7cdbc7011.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f4/ac1cb650b907590b42e3a2d5f595c7cdbc7011.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f4/ac1cb650b907590b42e3a2d5f595c7cdbc7011.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/59
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/59/811a72f3280625372e7e22d3ce4377c9ff1e85.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/59/811a72f3280625372e7e22d3ce4377c9ff1e85.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/59/811a72f3280625372e7e22d3ce4377c9ff1e85.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a2
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a2/19d682b37c3b5a3c707d96c18bbcc33da45e58.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a2/19d682b37c3b5a3c707d96c18bbcc33da45e58.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a2/19d682b37c3b5a3c707d96c18bbcc33da45e58.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26/77875d9115ae92a1cdd3ba8bd915b1ced440cf.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26/77875d9115ae92a1cdd3ba8bd915b1ced440cf.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/26/77875d9115ae92a1cdd3ba8bd915b1ced440cf.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d8/efcb20c91050613be4b363f6c85962b4782a88.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d8/efcb20c91050613be4b363f6c85962b4782a88.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d8/efcb20c91050613be4b363f6c85962b4782a88.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cb
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cb/a71058097fafe99436e6ce9a95ee8ef2fd777d.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cb/a71058097fafe99436e6ce9a95ee8ef2fd777d.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cb/a71058097fafe99436e6ce9a95ee8ef2fd777d.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/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)
+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/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa were not linked against libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=2677875d9115ae92a1cdd3ba8bd915b1ced440cf 489d8cdba827e4819d5fbf4ab59fe2cf4eead3f5 59811a72f3280625372e7e22d3ce4377 [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1667,22 +1856,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_kfreebsd-i386.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1323
+Build finished at 20160205-1625
Finished
────────
@@ -1699,108 +1888,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_kfreebsd-i386.changes:
+samtools_1.3-1_kfreebsd-i386.changes:
─────────────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-i386
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- 9f6cca37f8c8d1bb67dd2b8ed80f870853058798 384164 samtools-dbgsym_1.2-4_kfreebsd-i386.deb
- e9fa91a20011a3b12b028387f5fc9865b96aa75b 409052 samtools_1.2-4_kfreebsd-i386.deb
+ 82a33127c140bbec5daae39e5f171e9465f6a66b 425886 samtools-dbgsym_1.3-1_kfreebsd-i386.deb
+ dd903590521e1b6a53651ca3098d0710feff1352 253940 samtools_1.3-1_kfreebsd-i386.deb
Checksums-Sha256:
- cd3006cb9e4b49c1e0433ad771726b6e4c873083856f6d20ec7281e85f3f7db9 384164 samtools-dbgsym_1.2-4_kfreebsd-i386.deb
- 2f4f5f5ab5e9d2e92056908c183562a2005774660715004c411802b5ca7045b2 409052 samtools_1.2-4_kfreebsd-i386.deb
+ 63de29f1513133fce4fe1f38a55f9fdb7ca9ea12825986bbbaa277f9b5dbd4e6 425886 samtools-dbgsym_1.3-1_kfreebsd-i386.deb
+ 192ffa1d1c1817f36a63bdc962631aceb75d5f472ae69f5d20ab38f0b1a7c543 253940 samtools_1.3-1_kfreebsd-i386.deb
Files:
- 786527f96d922591fd1154b37b8033f7 384164 debug extra samtools-dbgsym_1.2-4_kfreebsd-i386.deb
- 393d48e7505a67e81630508c031d90ed 409052 science optional samtools_1.2-4_kfreebsd-i386.deb
+ a1eeb754d251384ac2c6ecdccc20c499 425886 debug extra samtools-dbgsym_1.3-1_kfreebsd-i386.deb
+ fedf67a33751f10ec87f63a19e79cdd9 253940 science optional samtools_1.3-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_kfreebsd-i386.deb
+samtools-dbgsym_1.3-1_kfreebsd-i386.deb
───────────────────────────────────────
new debian package, version 2.0.
- size 384164 bytes: control archive=824 bytes.
+ size 425886 bytes: control archive=822 bytes.
654 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 450
- Depends: samtools (= 1.2-4)
+ Installed-Size: 480
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 2677875d9115ae92a1cdd3ba8bd915b1ced440cf 489d8cdba827e4819d5fbf4ab59fe2cf4eead3f5 59811a72f3280625372e7e22d3ce4377c9ff1e85 a219d682b37c3b5a3c707d96c18bbcc33da45e58 cba71058097fafe99436e6ce9a95ee8ef2fd777d d8efcb20c91050613be4b363f6c85962b4782a88 f4ac1cb650b907590b42e3a2d5f595c7cdbc7011
+
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/26/
+-rw-r--r-- root/root 9580 2016-02-05 16:25 ./usr/lib/debug/.build-id/26/77875d9115ae92a1cdd3ba8bd915b1ced440cf.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/48/
+-rw-r--r-- root/root 401324 2016-02-05 16:25 ./usr/lib/debug/.build-id/48/9d8cdba827e4819d5fbf4ab59fe2cf4eead3f5.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/59/
+-rw-r--r-- root/root 9480 2016-02-05 16:25 ./usr/lib/debug/.build-id/59/811a72f3280625372e7e22d3ce4377c9ff1e85.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/a2/
+-rw-r--r-- root/root 9468 2016-02-05 16:25 ./usr/lib/debug/.build-id/a2/19d682b37c3b5a3c707d96c18bbcc33da45e58.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/cb/
+-rw-r--r-- root/root 16900 2016-02-05 16:25 ./usr/lib/debug/.build-id/cb/a71058097fafe99436e6ce9a95ee8ef2fd777d.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/d8/
+-rw-r--r-- root/root 7088 2016-02-05 16:25 ./usr/lib/debug/.build-id/d8/efcb20c91050613be4b363f6c85962b4782a88.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/lib/debug/.build-id/f4/
+-rw-r--r-- root/root 18168 2016-02-05 16:25 ./usr/lib/debug/.build-id/f4/ac1cb650b907590b42e3a2d5f595c7cdbc7011.debug
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2016-02-05 16:25 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_kfreebsd-i386.deb
────────────────────────────────
new debian package, version 2.0.
- size 409052 bytes: control archive=1615 bytes.
- 821 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ size 253940 bytes: control archive=1644 bytes.
+ 820 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1113
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 716
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1813,47 +2002,48 @@ samtools_1.2-4_kfreebsd-i386.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/bin/
+-rwxr-xr-x root/root 17956 2016-02-05 16:25 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9748 2016-02-05 16:25 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2016-02-05 16:25 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9768 2016-02-05 16:25 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5636 2016-02-05 16:25 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 444996 2016-02-05 16:25 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22116 2016-02-05 16:25 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 16:25 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 16:25 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 16:25 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 16:25 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 16:25 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1873,23 +2063,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-i386
-Build-Space: 16532
-Build-Time: 103
+Build-Space: 17088
+Build-Time: 105
Distribution: sid
Host Architecture: kfreebsd-i386
-Install-Time: 17
-Job: samtools_1.2-4
+Install-Time: 16
+Job: samtools_1.3-1
Machine Architecture: kfreebsd-i386
Package: samtools
-Package-Time: 150
-Source-Version: 1.2-4
-Space: 16532
+Package-Time: 155
+Source-Version: 1.3-1
+Space: 17088
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151221-1323
-Build needed 00:02:30, 16532k disc space
+Finished at 20160205-1625
+Build needed 00:02:35, 17088k disc space
Signature with key 'E3D16566' requested:
- signfile /home/buildd/build/samtools_1.2-4_kfreebsd-i386.changes E3D16566
+ signfile /home/buildd/build/samtools_1.3-1_kfreebsd-i386.changes E3D16566
Successfully signed changes file
diff --git a/m68k.log b/m68k.log
index ce28d6c..08fee77 100644
--- a/m68k.log
+++ b/m68k.log
@@ -1,106 +1,1054 @@
-sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on wario.physik.fu-berlin.de
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs91.physik.fu-berlin.de
-+==============================================================================+
-| samtools 1.2-4 (m68k) 19 Jan 2016 21:30 |
-+==============================================================================+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.3-1 (m68k) 05 Feb 2016 17:33 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
-Machine Architecture: m68k
+Machine Architecture: amd64
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)
+I: NOTICE: Log filtering will replace 'build/samtools-Rqi8nE/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-Rqi8nE' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-m68k-sbuild-5888e57e-5026-40c4-9c95-1b61c2d6d21d' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Ign:1 http://incoming.debian-ports.org/buildd unstable InRelease
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 ftp://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:4 http://incoming.debian-ports.org/buildd unstable Release [43.8 kB]
+Get:5 http://incoming.debian-ports.org/buildd unstable Release.gpg [836 B]
+Get:6 ftp://ftp.debian-ports.org/debian unstable InRelease [37.1 kB]
+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]
+Get:9 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-02-1445.56.pdiff [20.6 kB]
+Get:10 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-02-2051.26.pdiff [12.3 kB]
+Get:11 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-0247.20.pdiff [7814 B]
+Get:12 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-0847.44.pdiff [5373 B]
+Get:13 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-1452.45.pdiff [20.5 kB]
+Get:14 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-2047.23.pdiff [15.1 kB]
+Get:15 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-0247.46.pdiff [26.0 kB]
+Get:16 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-0851.05.pdiff [14.2 kB]
+Get:17 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-1446.17.pdiff [14.1 kB]
+Get:18 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-2131.08.pdiff [18.5 kB]
+Get:19 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:20 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-0254.43.pdiff [5835 B]
+Get:20 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-0254.43.pdiff [5835 B]
+Get:21 http://incoming.debian-ports.org/buildd unstable/main m68k Packages [68.6 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main m68k Packages [14.0 MB]
+Fetched 14.9 MB in 58s (256 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.
+W: No sandbox user '_apt' on the system, can not drop privileges
-+------------------------------------------------------------------------------+
-| Fetch source files |
-+------------------------------------------------------------------------------+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ 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 |
-+------------------------------------------------------------------------------+
+https://anonscm.debian.org/git/debian-med/samtools.git
+Please use:
+git clone https://anonscm.debian.org/git/debian-med/samtools.git
+to retrieve the latest (possibly unreleased) updates to the package.
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 25s (147 kB/s)
+Download complete and in download only mode
+
+Check architectures
+───────────────────
+
+
+Check dependencies
+──────────────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-NrfAPV/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Unsupported ioctl: cmd=0x40049409
+OK
+Get:1 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ Packages [528 B]
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ build-essential dpkg-dev fakeroot libdpkg-perl libfakeroot libperl5.22 perl
+ perl-modules-5.22
+Suggested packages:
+ debian-keyring perl-doc libterm-readline-gnu-perl
+ | libterm-readline-perl-perl
+Recommended packages:
+ libalgorithm-merge-perl libfile-fcntllock-perl netbase rename
+The following NEW packages will be installed:
+ build-essential dpkg-dev fakeroot libdpkg-perl libfakeroot libperl5.22 perl
+ perl-modules-5.22 sbuild-build-depends-core-dummy
+0 upgraded, 9 newly installed, 0 to remove and 12 not upgraded.
+Need to get 8835 kB/8836 kB of archives.
+After this operation, 38.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-NrfAPV/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
+Get:2 ftp://ftp.debian-ports.org/debian unstable/main m68k perl-modules-5.22 all 5.22.1-5 [2694 kB]
+Get:3 ftp://ftp.debian-ports.org/debian unstable/main m68k libperl5.22 m68k 5.22.1-5 [3183 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main m68k perl m68k 5.22.1-5 [237 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable/main m68k libdpkg-perl all 1.18.4 [1148 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unstable/main m68k dpkg-dev all 1.18.4 [1445 kB]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main m68k build-essential m68k 12.2 [7290 B]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main m68k libfakeroot m68k 1.20.2-1 [39.5 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main m68k fakeroot m68k 1.20.2-1 [82.1 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 8835 kB in 27s (327 kB/s)
+Selecting previously unselected package perl-modules-5.22.
+(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 10346 files and directories currently installed.)
+Preparing to unpack .../perl-modules-5.22_5.22.1-5_all.deb ...
+Unpacking perl-modules-5.22 (5.22.1-5) ...
+Selecting previously unselected package libperl5.22:m68k.
+Preparing to unpack .../libperl5.22_5.22.1-5_m68k.deb ...
+Unpacking libperl5.22:m68k (5.22.1-5) ...
+Selecting previously unselected package perl.
+Preparing to unpack .../perl_5.22.1-5_m68k.deb ...
+Unpacking perl (5.22.1-5) ...
+Selecting previously unselected package libdpkg-perl.
+Preparing to unpack .../libdpkg-perl_1.18.4_all.deb ...
+Unpacking libdpkg-perl (1.18.4) ...
+Selecting previously unselected package dpkg-dev.
+Preparing to unpack .../dpkg-dev_1.18.4_all.deb ...
+Unpacking dpkg-dev (1.18.4) ...
+Selecting previously unselected package build-essential.
+Preparing to unpack .../build-essential_12.2_m68k.deb ...
+Unpacking build-essential (12.2) ...
+Selecting previously unselected package libfakeroot:m68k.
+Preparing to unpack .../libfakeroot_1.20.2-1_m68k.deb ...
+Unpacking libfakeroot:m68k (1.20.2-1) ...
+Selecting previously unselected package fakeroot.
+Preparing to unpack .../fakeroot_1.20.2-1_m68k.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 perl-modules-5.22 (5.22.1-5) ...
+Setting up libperl5.22:m68k (5.22.1-5) ...
+Setting up perl (5.22.1-5) ...
+update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode
+Setting up libdpkg-perl (1.18.4) ...
+Setting up dpkg-dev (1.18.4) ...
+Setting up build-essential (12.2) ...
+Setting up libfakeroot:m68k (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) ...
+Processing triggers for libc-bin (2.21-7) ...
+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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-b6Bp9Q/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Unsupported ioctl: cmd=0x40049409
+OK
+Get:1 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ Packages [746 B]
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following additional packages will be installed:
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
+Suggested packages:
+ gnu-standards autoconf-doc libtool 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
+The following NEW packages will be installed:
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 36 newly installed, 0 to remove and 12 not upgraded.
+Need to get 19.9 MB/19.9 MB of archives.
+After this operation, 74.0 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-b6Bp9Q/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 ftp://ftp.debian-ports.org/debian unstable/main m68k bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 ftp://ftp.debian-ports.org/debian unstable/main m68k groff-base m68k 1.22.3-7 [1193 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main m68k bsdmainutils m68k 9.0.6+b1 [175 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable/main m68k libpipeline1 m68k 1.4.1-2 [24.3 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unstable/main m68k man-db m68k 2.7.5-1 [988 kB]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main m68k autoconf-archive all 20150925-1 [688 kB]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main m68k libsigsegv2 m68k 2.10-4 [28.0 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main m68k libunistring0 m68k 0.9.3-5.2 [255 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main m68k libmagic1 m68k 1:5.25-2 [250 kB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main m68k file m68k 1:5.25-2 [60.7 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main m68k gettext-base m68k 0.19.6-1 [119 kB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main m68k libicu55 m68k 55.1-7 [7359 kB]
+Get:14 ftp://ftp.debian-ports.org/debian unstable/main m68k libxml2 m68k 2.9.3+dfsg1-1 [788 kB]
+Get:15 ftp://ftp.debian-ports.org/debian unstable/main m68k m4 m68k 1.4.17-5 [238 kB]
+Get:16 ftp://ftp.debian-ports.org/debian unstable/main m68k autoconf all 2.69-9 [338 kB]
+Get:17 ftp://ftp.debian-ports.org/debian unstable/main m68k autotools-dev all 20150820.1 [71.7 kB]
+Get:18 ftp://ftp.debian-ports.org/debian unstable/main m68k automake all 1:1.15-3 [735 kB]
+Get:19 ftp://ftp.debian-ports.org/debian unstable/main m68k libffi6 m68k 3.2.1-4 [17.1 kB]
+Get:20 ftp://ftp.debian-ports.org/debian unstable/main m68k libglib2.0-0 m68k 2.46.2-1 [2506 kB]
+Get:21 ftp://ftp.debian-ports.org/debian unstable/main m68k libcroco3 m68k 0.6.11-1 [133 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main m68k gettext m68k 0.19.6-1 [1376 kB]
+Get:23 ftp://ftp.debian-ports.org/debian unstable/main m68k intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 ftp://ftp.debian-ports.org/debian unstable/main m68k po-debconf all 1.0.19 [249 kB]
+Get:25 ftp://ftp.debian-ports.org/debian unstable/main m68k libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 ftp://ftp.debian-ports.org/debian unstable/main m68k libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main m68k libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 ftp://ftp.debian-ports.org/debian unstable/main m68k dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 ftp://ftp.debian-ports.org/debian unstable/main m68k debhelper all 9.20160115 [827 kB]
+Get:30 ftp://ftp.debian-ports.org/debian unstable/main m68k libhts1 m68k 1.3-1 [206 kB]
+Get:31 ftp://ftp.debian-ports.org/debian unstable/main m68k libhts-dev m68k 1.3-1 [260 kB]
+Get:32 ftp://ftp.debian-ports.org/debian unstable/main m68k libio-pty-perl m68k 1:1.08-1.1+b1 [33.6 kB]
+Get:33 ftp://ftp.debian-ports.org/debian unstable/main m68k libtinfo-dev m68k 6.0+20151024-2 [65.7 kB]
+Get:34 ftp://ftp.debian-ports.org/debian unstable/main m68k libncurses5-dev m68k 6.0+20151024-2 [152 kB]
+Get:35 ftp://ftp.debian-ports.org/debian unstable/main m68k tabix m68k 1.3-1 [184 kB]
+Get:36 ftp://ftp.debian-ports.org/debian unstable/main m68k zlib1g-dev m68k 1:1.2.8.dfsg-2+b1 [196 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 19.9 MB in 1min 22s (240 kB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12492 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_1.22.3-7_m68k.deb ...
+Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6+b1_m68k.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
+Selecting previously unselected package libpipeline1:m68k.
+Preparing to unpack .../libpipeline1_1.4.1-2_m68k.deb ...
+Unpacking libpipeline1:m68k (1.4.1-2) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.5-1_m68k.deb ...
+Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:m68k.
+Preparing to unpack .../libsigsegv2_2.10-4_m68k.deb ...
+Unpacking libsigsegv2:m68k (2.10-4) ...
+Selecting previously unselected package libunistring0:m68k.
+Preparing to unpack .../libunistring0_0.9.3-5.2_m68k.deb ...
+Unpacking libunistring0:m68k (0.9.3-5.2) ...
+Selecting previously unselected package libmagic1:m68k.
+Preparing to unpack .../libmagic1_1%3a5.25-2_m68k.deb ...
+Unpacking libmagic1:m68k (1:5.25-2) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-2_m68k.deb ...
+Unpacking file (1:5.25-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_m68k.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:m68k.
+Preparing to unpack .../libicu55_55.1-7_m68k.deb ...
+Unpacking libicu55:m68k (55.1-7) ...
+Selecting previously unselected package libxml2:m68k.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_m68k.deb ...
+Unpacking libxml2:m68k (2.9.3+dfsg1-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../archives/m4_1.4.17-5_m68k.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
+Selecting previously unselected package libffi6:m68k.
+Preparing to unpack .../libffi6_3.2.1-4_m68k.deb ...
+Unpacking libffi6:m68k (3.2.1-4) ...
+Selecting previously unselected package libglib2.0-0:m68k.
+Preparing to unpack .../libglib2.0-0_2.46.2-1_m68k.deb ...
+Unpacking libglib2.0-0:m68k (2.46.2-1) ...
+Selecting previously unselected package libcroco3:m68k.
+Preparing to unpack .../libcroco3_0.6.11-1_m68k.deb ...
+Unpacking libcroco3:m68k (0.6.11-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_m68k.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_1.0.19_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_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
+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_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
+Selecting previously unselected package libhts1:m68k.
+Preparing to unpack .../libhts1_1.3-1_m68k.deb ...
+Unpacking libhts1:m68k (1.3-1) ...
+Selecting previously unselected package libhts-dev:m68k.
+Preparing to unpack .../libhts-dev_1.3-1_m68k.deb ...
+Unpacking libhts-dev:m68k (1.3-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_m68k.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
+Selecting previously unselected package libtinfo-dev:m68k.
+Preparing to unpack .../libtinfo-dev_6.0+20151024-2_m68k.deb ...
+Unpacking libtinfo-dev:m68k (6.0+20151024-2) ...
+Selecting previously unselected package libncurses5-dev:m68k.
+Preparing to unpack .../libncurses5-dev_6.0+20151024-2_m68k.deb ...
+Unpacking libncurses5-dev:m68k (6.0+20151024-2) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../archives/tabix_1.3-1_m68k.deb ...
+Unpacking tabix (1.3-1) ...
+Selecting previously unselected package zlib1g-dev:m68k.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_m68k.deb ...
+Unpacking zlib1g-dev:m68k (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 (2.21-7) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-7) ...
+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:m68k (1.4.1-2) ...
+Setting up man-db (2.7.5-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:m68k (2.10-4) ...
+Setting up libunistring0:m68k (0.9.3-5.2) ...
+Setting up libmagic1:m68k (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:m68k (55.1-7) ...
+Setting up libxml2:m68k (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up libffi6:m68k (3.2.1-4) ...
+Setting up libglib2.0-0:m68k (2.46.2-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:m68k (0.6.11-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libhts1:m68k (1.3-1) ...
+Setting up libhts-dev:m68k (1.3-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:m68k (6.0+20151024-2) ...
+Setting up libncurses5-dev:m68k (6.0+20151024-2) ...
+Setting up tabix (1.3-1) ...
+Setting up zlib1g-dev:m68k (1:1.2.8.dfsg-2+b1) ...
+Setting up debhelper (9.20160115) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 4.2.0-0.bpo.1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-6 gcc-5_5.3.1-6 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-6 libstdc++6_5.3.1-6 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-6 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debian-ports-archive-keyring_2016.01.25 debi [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
+dpkg-source: info: applying mayhem.patch
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=nobench nocheck
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-m68k-sbuild
+SCHROOT_CHROOT_NAME=sid-m68k-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=122
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-m68k-sbuild-5888e57e-5026-40c4-9c95-1b61c2d6d21d
+SCHROOT_UID=114
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_SESSION_ID=c7578
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.3
+dpkg-buildpackage: host architecture m68k
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ debian/rules override_dh_auto_clean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+dh_auto_clean --
+ make -j1 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
+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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
+rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -rf debian/.debhelper/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=m68k-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/m68k-linux-gnu --libexecdir=\${prefix}/lib/m68k-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j1 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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
+/usr/bin/ar: `u' modifier ignored since `D' is the default (see `U')
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ BGZIP=/usr/bin/bgzip
+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
+ install -d debian/samtools
+ make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
+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 misc/wgsim.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 test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
+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_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/
+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
+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
+ 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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
+ dh_installman -a -O--parallel
+ 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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.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
+ 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/NEWS.Debian 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/NEWS.Debian 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/m68k-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/dbgsym-root/usr/lib/debug/.build-id/f2
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/a02531cb545bab15b2eef0fc230c556559bb43.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/a02531cb545bab15b2eef0fc230c556559bb43.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/a02531cb545bab15b2eef0fc230c556559bb43.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/5bb2d18fef99ae5571a5dd014167a25d105107.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/5bb2d18fef99ae5571a5dd014167a25d105107.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/15/5bb2d18fef99ae5571a5dd014167a25d105107.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8f/7580c5b0054b8a61fe2b9c16ecd65cfe485fb4.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8f/7580c5b0054b8a61fe2b9c16ecd65cfe485fb4.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8f/7580c5b0054b8a61fe2b9c16ecd65cfe485fb4.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/b46743d1b79752a4d794bc7c3c16eb210ad501.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/b46743d1b79752a4d794bc7c3c16eb210ad501.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/af/b46743d1b79752a4d794bc7c3c16eb210ad501.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/7fb45759d6c803205044e3d96926a8e38885a4.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/7fb45759d6c803205044e3d96926a8e38885a4.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/7fb45759d6c803205044e3d96926a8e38885a4.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/58f4f23900023f89eba932ddfb33b1e9f1678a.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/58f4f23900023f89eba932ddfb33b1e9f1678a.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/52/58f4f23900023f89eba932ddfb33b1e9f1678a.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84/5869bef128cdf29582738e3718f2b02f2d1fc0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84/5869bef128cdf29582738e3718f2b02f2d1fc0.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84/5869bef128cdf29582738e3718f2b02f2d1fc0.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/wgsim 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/md5fa debian/samtools/usr/bin/samtools were not linked against ld.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim 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/md5fa debian/samtools/usr/bin/samtools were not linked against libdl.so.2 (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/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=155bb2d18fef99ae5571a5dd014167a25d105107 477fb45759d6c803205044e3d96926a8e38885a4 5258f4f23900023f89eba932ddfb33b1 [...]
+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/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 ${perl:Depends}
+ chmod 0644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_m68k.deb'.
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.3-1_m68k.deb'.
+ dpkg-genchanges -B -mdebian/m68k buildd <buildd-vs91 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3-1_m68k.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-buildpackage: binary-only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20160205-1748
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.3-1_m68k.changes:
+────────────────────────────
+
+Format: 1.8
+Date: Fri, 05 Feb 2016 08:32:40 +0000
+Source: samtools
+Binary: samtools samtools-test
+Architecture: m68k
+Version: 1.3-1
+Distribution: sid
+Urgency: medium
+Maintainer: debian/m68k buildd <buildd-vs91 at glaubitz.dialup.fu-berlin.de>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Changes:
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
+ .
+ [ Sascha Steinbiss ]
+ * Team upload
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
+ * Fix spelling
+Checksums-Sha1:
+ 71fe9c8c0e937239922a9b8e89771243dae239c2 428462 samtools-dbgsym_1.3-1_m68k.deb
+ 2c52edcb2549b71faa66aa947dc95ddb1940d611 211086 samtools_1.3-1_m68k.deb
+Checksums-Sha256:
+ b2265f275ead2ffc45bddc6d7a9066eecf9431354a92e2b21a486c1df407d23b 428462 samtools-dbgsym_1.3-1_m68k.deb
+ aea7269ce2b4da7b207f831742b0b0fe7618b7e73ecc017811b0b0fc370f3eed 211086 samtools_1.3-1_m68k.deb
+Files:
+ 7c14dea6ff0cfa02926b630573121c0d 428462 debug extra samtools-dbgsym_1.3-1_m68k.deb
+ 7ae48f62c21220b34351e60b3ab1bec5 211086 science optional samtools_1.3-1_m68k.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-dbgsym_1.3-1_m68k.deb
+──────────────────────────────
+
+ new debian package, version 2.0.
+ size 428462 bytes: control archive=822 bytes.
+ 645 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.3-1
+ Architecture: m68k
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 483
+ Depends: samtools (= 1.3-1)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 155bb2d18fef99ae5571a5dd014167a25d105107 477fb45759d6c803205044e3d96926a8e38885a4 5258f4f23900023f89eba932ddfb33b1e9f1678a 845869bef128cdf29582738e3718f2b02f2d1fc0 8f7580c5b0054b8a61fe2b9c16ecd65cfe485fb4 afb46743d1b79752a4d794bc7c3c16eb210ad501 f2a02531cb545bab15b2eef0fc230c556559bb43
+
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/15/
+-rw-r--r-- root/root 18984 2016-02-05 17:48 ./usr/lib/debug/.build-id/15/5bb2d18fef99ae5571a5dd014167a25d105107.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/47/
+-rw-r--r-- root/root 9292 2016-02-05 17:48 ./usr/lib/debug/.build-id/47/7fb45759d6c803205044e3d96926a8e38885a4.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/52/
+-rw-r--r-- root/root 6948 2016-02-05 17:48 ./usr/lib/debug/.build-id/52/58f4f23900023f89eba932ddfb33b1e9f1678a.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/84/
+-rw-r--r-- root/root 16616 2016-02-05 17:48 ./usr/lib/debug/.build-id/84/5869bef128cdf29582738e3718f2b02f2d1fc0.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/8f/
+-rw-r--r-- root/root 9248 2016-02-05 17:48 ./usr/lib/debug/.build-id/8f/7580c5b0054b8a61fe2b9c16ecd65cfe485fb4.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/af/
+-rw-r--r-- root/root 9240 2016-02-05 17:48 ./usr/lib/debug/.build-id/af/b46743d1b79752a4d794bc7c3c16eb210ad501.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/lib/debug/.build-id/f2/
+-rw-r--r-- root/root 402780 2016-02-05 17:48 ./usr/lib/debug/.build-id/f2/a02531cb545bab15b2eef0fc230c556559bb43.debug
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-05 17:48 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_m68k.deb
+───────────────────────
+
+ new debian package, version 2.0.
+ size 211086 bytes: control archive=1642 bytes.
+ 805 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
+ Package: samtools
+ Version: 1.3-1
+ Architecture: m68k
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 636
+ Depends: libc6 (>= 2.7), libhts1 (>= 1.3), 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 2016-02-05 17:48 ./
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/bin/
+-rwxr-xr-x root/root 17824 2016-02-05 17:48 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 22:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 22:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 22:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 22:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9620 2016-02-05 17:48 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9620 2016-02-05 17:48 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9640 2016-02-05 17:48 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9604 2016-02-05 17:48 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 22:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 22:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 22:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 22:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 362968 2016-02-05 17:48 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 22:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 22:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 22:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 22:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17900 2016-02-05 17:48 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 22:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 22:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 22:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 15:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 15:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 15:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 15:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 15:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 15:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 17:48 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 17:48 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 17:48 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 17:48 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 17:48 ./usr/share/man/man1/wgsim.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
-E: Failed to fetch source files
-+------------------------------------------------------------------------------+
-| Summary |
-+------------------------------------------------------------------------------+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: m68k
-Build-Space: 0
-Build-Time: 0
+Build-Space: 16184
+Build-Time: 583
Distribution: sid
-Fail-Stage: fetch-src
Host Architecture: m68k
-Install-Time: 0
-Job: samtools_1.2-4
-Machine Architecture: m68k
+Install-Time: 245
+Job: samtools_1.3-1
+Machine Architecture: amd64
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
+Package-Time: 937
+Source-Version: 1.3-1
+Space: 16184
+Status: successful
+Version: 1.3-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20160205-1748
+Build needed 00:15:37, 16184k disc space
+Signature with key '2793F01F' requested:
+ signfile /var/lib/buildd/build/samtools_1.3-1_m68k.changes 2793F01F
+
+Successfully signed changes file
diff --git a/mips64el.log b/mips64el.log
index 131db2d..9eac107 100644
--- a/mips64el.log
+++ b/mips64el.log
@@ -1,41 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on argos.ayous.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on clash.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (mips64el) 22 Dec 2015 12:35 ║
+║ samtools 1.3-1 (mips64el) 06 Feb 2016 00:35 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mips64el
Build Architecture: mips64el
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-UGgexm/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-UGgexm' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mips64el-sbuild-4e109306-d423-4cd8-8e9e-0873066db43f' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org/debian unstable InRelease [265 kB]
-Get:2 http://mirror.ayous.org/debian unstable InRelease [265 kB]
+Get:1 http://mirrors.tuna.tsinghua.edu.cn/debian unstable InRelease [278 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [278 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)
+Get:4 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main Sources [8513 kB]
+Get:5 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/contrib Sources [61.4 kB]
+Get:6 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/non-free Sources [106 kB]
+Get:7 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el Packages [7691 kB]
+Get:8 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/contrib mips64el Packages [43.9 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main mips64el Packages [161 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mips64el Packages [32 B]
+Get:14 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:17 http://ftp.debian.org/debian unstable/main mips64el Packages [7691 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib mips64el Packages [43.9 kB]
+Fetched 33.8 MB in 27s (1216 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -56,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 2s (1722 kB/s)
Download complete and in download only mode
Check architectures
@@ -78,16 +82,16 @@ 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-GhBar7/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-O3tI9s/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -102,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
-Need to get 0 B/772 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded.
+Need to get 0 B/764 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]
+Get:1 file:/«BUILDDIR»/resolver-O3tI9s/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 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%
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(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.)
+(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 ... 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 ... 12334 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, 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'.
+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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-NKxur3/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Sources [374 B]
+Get:5 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ Packages [632 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -138,77 +142,88 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 18 not upgraded.
+Need to get 20.5 MB/20.5 MB of archives.
+After this operation, 80.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-NKxur3/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [878 B]
+Get:2 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el groff-base mips64el 1.22.3-7 [1276 kB]
+Get:4 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el bsdmainutils mips64el 9.0.6+b2 [188 kB]
+Get:5 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libpipeline1 mips64el 1.4.1-2 [26.6 kB]
+Get:6 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el man-db mips64el 2.7.5-1 [990 kB]
+Get:7 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libmagic1 mips64el 1:5.25-2 [255 kB]
+Get:9 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el file mips64el 1:5.25-2 [61.9 kB]
+Get:10 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el gettext-base mips64el 0.19.7-2 [115 kB]
+Get:11 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libicu55 mips64el 55.1-7 [7576 kB]
+Get:12 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libxml2 mips64el 2.9.3+dfsg1-1 [830 kB]
+Get:13 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libsigsegv2 mips64el 2.10-4+b1 [29.1 kB]
+Get:14 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el m4 mips64el 1.4.17-5 [253 kB]
+Get:15 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autoconf all 2.69-9 [338 kB]
+Get:16 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autotools-dev all 20150820.1 [71.7 kB]
+Get:17 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el automake all 1:1.15-3 [735 kB]
+Get:18 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libffi6 mips64el 3.2.1-4 [20.7 kB]
+Get:19 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libglib2.0-0 mips64el 2.46.2-3 [2482 kB]
+Get:20 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libcroco3 mips64el 0.6.11-1 [131 kB]
+Get:21 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libunistring0 mips64el 0.9.3-5.2+b1 [258 kB]
+Get:22 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el gettext mips64el 0.19.7-2 [1445 kB]
+Get:23 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el po-debconf all 1.0.19 [249 kB]
+Get:25 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el debhelper all 9.20160115 [827 kB]
+Get:30 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libhts1 mips64el 1.3-1 [227 kB]
+Get:31 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libhts-dev mips64el 1.3-1 [328 kB]
+Get:32 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libio-pty-perl mips64el 1:1.08-1.1+b1 [31.6 kB]
+Get:33 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtinfo-dev mips64el 6.0+20151024-2 [83.5 kB]
+Get:34 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libncurses5-dev mips64el 6.0+20151024-2 [184 kB]
+Get:35 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el tabix mips64el 1.3-1 [237 kB]
+Get:36 http://mirrors.tuna.tsinghua.edu.cn/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 18.3 MB in 2s (6759 kB/s)
+Fetched 20.5 MB in 1s (10.7 MB/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 ... 12321 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 ... 12334 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_1.22.3-4_mips64el.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_mips64el.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_mips64el.deb ...
+Unpacking libpipeline1:mips64el (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_mips64el.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
Selecting previously unselected package libmagic1:mips64el.
Preparing to unpack .../libmagic1_1%3a5.25-2_mips64el.deb ...
Unpacking libmagic1:mips64el (1:5.25-2) ...
@@ -216,20 +231,35 @@ Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_mips64el.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.6-1_mips64el.deb ...
-Unpacking gettext-base (0.19.6-1) ...
+Preparing to unpack .../gettext-base_0.19.7-2_mips64el.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:mips64el.
-Preparing to unpack .../libicu55_55.1-6_mips64el.deb ...
-Unpacking libicu55:mips64el (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_mips64el.deb ...
+Unpacking libicu55:mips64el (55.1-7) ...
Selecting previously unselected package libxml2:mips64el.
Preparing to unpack .../libxml2_2.9.3+dfsg1-1_mips64el.deb ...
Unpacking libxml2:mips64el (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libsigsegv2:mips64el.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_mips64el.deb ...
+Unpacking libsigsegv2:mips64el (2.10-4+b1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../m4_1.4.17-5_mips64el.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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_2.46.2-1_mips64el.deb ...
-Unpacking libglib2.0-0:mips64el (2.46.2-1) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_mips64el.deb ...
+Unpacking libglib2.0-0:mips64el (2.46.2-3) ...
Selecting previously unselected package libcroco3:mips64el.
Preparing to unpack .../libcroco3_0.6.11-1_mips64el.deb ...
Unpacking libcroco3:mips64el (0.6.11-1) ...
@@ -237,35 +267,35 @@ 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) ...
Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.6-1_mips64el.deb ...
-Unpacking gettext (0.19.6-1) ...
+Preparing to unpack .../gettext_0.19.7-2_mips64el.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:mips64el.
-Preparing to unpack .../libhts1_1.2.1-2_mips64el.deb ...
-Unpacking libhts1:mips64el (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_mips64el.deb ...
+Unpacking libhts1:mips64el (1.3-1) ...
Selecting previously unselected package libhts-dev:mips64el.
-Preparing to unpack .../libhts-dev_1.2.1-2_mips64el.deb ...
-Unpacking libhts-dev:mips64el (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_mips64el.deb ...
+Unpacking libhts-dev:mips64el (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_mips64el.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -276,59 +306,66 @@ Selecting previously unselected package libncurses5-dev:mips64el.
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_1.2.1-2_mips64el.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../tabix_1.3-1_mips64el.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:mips64el (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
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 (55.1-6) ...
+Setting up gettext-base (0.19.7-2) ...
+Setting up libicu55:mips64el (55.1-7) ...
Setting up libxml2:mips64el (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:mips64el (2.10-4+b1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:mips64el (3.2.1-4) ...
-Setting up libglib2.0-0:mips64el (2.46.2-1) ...
+Setting up libglib2.0-0:mips64el (2.46.2-3) ...
No schema files found: doing nothing.
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 gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:mips64el (1.3-1) ...
+Setting up libhts-dev:mips64el (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:mips64el (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-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- [...]
+Kernel: Linux 4.1.0-0.bpo.1-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.25.90.20160101-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.25.90.20160101-2 bsdmainutils_9.0.6+b2 bsdutils_1:2.27.1-3 build-essential_12.1+b1 bzip2_1.0.6-8+b1 coreutils_8.24-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debfoster_2.7-2 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutil [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -339,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -365,10 +401,10 @@ 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=802
+SCHROOT_GID=114
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mips64el-sbuild-eef44738-cc75-4fa0-bcb9-ec5938b7d505
-SCHROOT_UID=802
+SCHROOT_SESSION_ID=sid-mips64el-sbuild-4e109306-d423-4cd8-8e9e-0873066db43f
+SCHROOT_UID=109
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
@@ -377,24 +413,31 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture mips64el
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j4 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j4 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -416,189 +459,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=mips64el-linux-gnuabi64 --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/mips64el-linux-gnuabi64 --libexecdir=\${prefix}/lib/mips64el-linux-gnuabi64 --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- 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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
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/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 -j4 test 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/eHILIcLGar/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/fQYixOz32a/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/eHILIcLGar/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/fQYixOz32a/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/eHILIcLGar/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/fQYixOz32a/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/eHILIcLGar/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/fQYixOz32a/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/eHILIcLGar/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/fQYixOz32a/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/eHILIcLGar/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/fQYixOz32a/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/eHILIcLGar/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/fQYixOz32a/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/eHILIcLGar/mpileup.bam.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/fQYixOz32a/mpileup.bam.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/fQYixOz32a/mpileup.bam.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/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/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/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/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/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/eHILIcLGar/mpileup.cram.list -f /tmp/eHILIcLGar/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/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:1050-1060 /tmp/fQYixOz32a/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:1050-1060 /tmp/fQYixOz32a/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -637,7 +735,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -667,7 +769,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -684,9 +794,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -718,6 +826,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -820,83 +932,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/eHILIcLGar/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/eHILIcLGar/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/eHILIcLGar/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/eHILIcLGar/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/eHILIcLGar/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/eHILIcLGar/view.001.fogn (CRAM input) .. ok
+ 49: Filter -R /tmp/fQYixOz32a/view.001.fogn (SAM input) .. ok
- 55: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (SAM input).. ok
+ 50: Count -R /tmp/fQYixOz32a/view.001.fogn (SAM input) .. ok
- 56: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (SAM input).. ok
+ 51: Filter -R /tmp/fQYixOz32a/view.001.fogn (BAM input) .. ok
- 57: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (BAM input).. ok
+ 52: Count -R /tmp/fQYixOz32a/view.001.fogn (BAM input) .. ok
- 58: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (BAM input).. ok
+ 53: Filter -R /tmp/fQYixOz32a/view.001.fogn (CRAM input) .. ok
- 59: Filter -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (CRAM input).. ok
+ 54: Count -R /tmp/fQYixOz32a/view.001.fogn (CRAM input) .. ok
- 60: Count -R /tmp/eHILIcLGar/view.001.fogn -r grp2 (CRAM input).. ok
+ 55: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (SAM input).. ok
- 61: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (SAM input).. ok
+ 56: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (SAM input).. ok
- 62: Count -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (SAM input).. ok
+ 57: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (BAM input).. ok
- 63: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (BAM input).. ok
+ 58: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (BAM input).. ok
- 64: Count -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (BAM input).. ok
+ 59: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (CRAM input).. ok
- 65: Filter -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (CRAM input).. ok
+ 60: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/eHILIcLGar/view.001.fogn (CRAM input).. ok
+ 61: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (SAM input).. ok
- 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
+ 62: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (SAM input).. ok
+ 63: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
-
+ 64: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
+ 65: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (CRAM input).. ok
-.. expected failure
+ 67: Filter -l Library 2 (SAM input) .. ok
- 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
+ 68: Count -l Library 2 (SAM input) .. ok
+ 69: Filter -l Library 2 (BAM input) .. ok
-.. expected failure
-
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
- 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
+ 71: Filter -l Library 2 (CRAM input) .. ok
-
-.. expected failure
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1316,132 +1398,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 6: cat CRAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 7: cat BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1453,12 +1540,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/YKE3bspd73 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qnHqAQUUUz - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1481,24 +1598,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1508,6 +1692,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1524,22 +1717,21 @@ dh binary-arch --parallel
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
+ prefix=/usr
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 -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1561,16 +1753,17 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
@@ -1584,8 +1777,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1601,58 +1794,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9cadb7125f183fc6120c97b7ff7870e794675c.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9cadb7125f183fc6120c97b7ff7870e794675c.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9cadb7125f183fc6120c97b7ff7870e794675c.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/78
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/78/f1d518d33d223cea49a2c6ce104461c506e184.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/78/f1d518d33d223cea49a2c6ce104461c506e184.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/78/f1d518d33d223cea49a2c6ce104461c506e184.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9e/ec5d307751afab496de7cd7be73f17c348d1c3.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9e/ec5d307751afab496de7cd7be73f17c348d1c3.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9e/ec5d307751afab496de7cd7be73f17c348d1c3.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a4
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a4/c88b9010583384e72fac6d69f356b326427988.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a4/c88b9010583384e72fac6d69f356b326427988.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a4/c88b9010583384e72fac6d69f356b326427988.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c9/5c96226e3a6d2368a5e332faa27d56125710dc.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c9/5c96226e3a6d2368a5e332faa27d56125710dc.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c9/5c96226e3a6d2368a5e332faa27d56125710dc.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e3
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e3/02c504a08ff7a51e899a09b10f161540a66c27.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e3/02c504a08ff7a51e899a09b10f161540a66c27.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e3/02c504a08ff7a51e899a09b10f161540a66c27.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/f5ba02e2233438e2e5504f9ae3a58cf668aff9.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/f5ba02e2233438e2e5504f9ae3a58cf668aff9.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ce/f5ba02e2233438e2e5504f9ae3a58cf668aff9.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim were not linked against libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=5d9cadb7125f183fc6120c97b7ff7870e794675c 78f1d518d33d223cea49a2c6ce104461c506e184 9eec5d307751afab496de7cd7be73f17 [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1662,22 +1856,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_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-deb: building package 'samtools' in '../samtools_1.3-1_mips64el.deb'.
+ dpkg-genchanges -B -mmips64el Build Daemon (clash) <buildd_mips64el-clash at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151222-1334
+Build finished at 20160206-0133
Finished
────────
@@ -1694,107 +1888,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_mips64el.changes:
+samtools_1.3-1_mips64el.changes:
────────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: mips64el
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
-Maintainer: mipsel Build Daemon (argos) <buildd_mipsel-argos at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Maintainer: mips64el Build Daemon (clash) <buildd_mips64el-clash at buildd.debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* 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
+ db1a8257413ce2dabffd584224fda38024ea7b9c 462710 samtools-dbgsym_1.3-1_mips64el.deb
+ 4425c2189e5d7fe2e467bc712c801dc9b314d627 240530 samtools_1.3-1_mips64el.deb
Checksums-Sha256:
- 7ce3a5d812177fc3dd1ef99cbbc4e27837900cf2c263fa61bc3fb14b460fe274 415882 samtools-dbgsym_1.2-4_mips64el.deb
- 34f8720f0b783d5877b09ed70043a857f7aa5ed5df5c697821e23e48a0017a7e 387522 samtools_1.2-4_mips64el.deb
+ 6a3ecd015ccde15b8863f9e42d224d48c8168c796e09a3215141a0e266f72fce 462710 samtools-dbgsym_1.3-1_mips64el.deb
+ 7248260663b92e55b697a6c9efebc79699f4449ba2b3c68d0426318ee7c09ba4 240530 samtools_1.3-1_mips64el.deb
Files:
- d1a1b925ba4cc7c025f9b259f7f62445 415882 debug extra samtools-dbgsym_1.2-4_mips64el.deb
- 4faabfad6e673e624081417c50f3a4ac 387522 science optional samtools_1.2-4_mips64el.deb
+ 733bfe239bb53bb3a22f9e4ec54ba491 462710 debug extra samtools-dbgsym_1.3-1_mips64el.deb
+ 06062eae25f2dabedff5f557c3c61871 240530 science optional samtools_1.3-1_mips64el.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_mips64el.deb
+samtools-dbgsym_1.3-1_mips64el.deb
──────────────────────────────────
new debian package, version 2.0.
- size 415882 bytes: control archive=822 bytes.
+ size 462710 bytes: control archive=821 bytes.
650 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: mips64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1482
- Depends: samtools (= 1.2-4)
+ Installed-Size: 1063
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 5d9cadb7125f183fc6120c97b7ff7870e794675c 78f1d518d33d223cea49a2c6ce104461c506e184 9eec5d307751afab496de7cd7be73f17c348d1c3 a4c88b9010583384e72fac6d69f356b326427988 c95c96226e3a6d2368a5e332faa27d56125710dc cef5ba02e2233438e2e5504f9ae3a58cf668aff9 e302c504a08ff7a51e899a09b10f161540a66c27
+
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/5d/
+-rw-r--r-- root/root 51664 2016-02-06 01:33 ./usr/lib/debug/.build-id/5d/9cadb7125f183fc6120c97b7ff7870e794675c.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/78/
+-rw-r--r-- root/root 14512 2016-02-06 01:33 ./usr/lib/debug/.build-id/78/f1d518d33d223cea49a2c6ce104461c506e184.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/9e/
+-rw-r--r-- root/root 20832 2016-02-06 01:33 ./usr/lib/debug/.build-id/9e/ec5d307751afab496de7cd7be73f17c348d1c3.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/a4/
+-rw-r--r-- root/root 20032 2016-02-06 01:33 ./usr/lib/debug/.build-id/a4/c88b9010583384e72fac6d69f356b326427988.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/c9/
+-rw-r--r-- root/root 20032 2016-02-06 01:33 ./usr/lib/debug/.build-id/c9/5c96226e3a6d2368a5e332faa27d56125710dc.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/ce/
+-rw-r--r-- root/root 903744 2016-02-06 01:33 ./usr/lib/debug/.build-id/ce/f5ba02e2233438e2e5504f9ae3a58cf668aff9.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/lib/debug/.build-id/e3/
+-rw-r--r-- root/root 37768 2016-02-06 01:33 ./usr/lib/debug/.build-id/e3/02c504a08ff7a51e899a09b10f161540a66c27.debug
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-06 01:33 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_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
+ size 240530 bytes: control archive=1634 bytes.
+ 810 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
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)
+ Installed-Size: 778
+ Depends: libc6 (>= 2.21), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1807,47 +2002,48 @@ samtools_1.2-4_mips64el.deb
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
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/bin/
+-rwxr-xr-x root/root 23336 2016-02-06 01:33 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-16 05:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-16 05:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-16 05:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-16 05:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 11080 2016-02-06 01:33 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 11080 2016-02-06 01:33 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 15112 2016-02-06 01:33 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10912 2016-02-06 01:33 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-16 05:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-16 05:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-16 05:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-16 05:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 476328 2016-02-06 01:33 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-16 05:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-16 05:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-16 05:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-16 05:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 36192 2016-02-06 01:33 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-16 05:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-16 05:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-16 05:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 22:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 22:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 22:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 22:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 22:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 22:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-06 01:33 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-06 01:33 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-06 01:33 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-06 01:33 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-06 01:33 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1867,19 +2063,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mips64el
-Build-Space: 21348
-Build-Time: 3297
+Build-Space: 22128
+Build-Time: 3326
Distribution: sid
Host Architecture: mips64el
-Install-Time: 68
-Job: samtools_1.2-4
+Install-Time: 57
+Job: samtools_1.3-1
Machine Architecture: mipsel
Package: samtools
-Package-Time: 3496
-Source-Version: 1.2-4
-Space: 21348
+Package-Time: 3472
+Source-Version: 1.3-1
+Space: 22128
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151222-1334
-Build needed 00:58:16, 21348k disc space
+Finished at 20160206-0133
+Build needed 00:57:52, 22128k disc space
diff --git a/mipsel.log b/mipsel.log
index f179514..9f36a52 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,45 +1,45 @@
-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 mipsel-aql-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (mipsel) 21 Dec 2015 13:23 ║
+║ samtools 1.3-1 (mipsel) 05 Feb 2016 17:21 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mipsel
Build Architecture: mipsel
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-LZOcDf/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-LZOcDf' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-ab539df7-da35-49a8-9d8f-c2d942ce0cc8' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.uk.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.uk.debian.org/debian unstable/main Sources [8513 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/non-free Sources [106 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main mipsel Packages [7878 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [181 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [2228 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main mipsel Packages [175 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mipsel Packages [1112 B]
+Get:14 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:15 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:16 http://ftp.debian.org/debian unstable/main mipsel Packages [7878 kB]
+Get:17 http://ftp.uk.debian.org/debian unstable/contrib mipsel Packages [46.2 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib mipsel Packages [46.2 kB]
+Fetched 34.2 MB in 37s (902 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 0s (7059 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-v1gSqC/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-b0HCFz/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-b0HCFz/apt_archive ./ Packages [528 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 12 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 10 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]
+Get:1 file:/«BUILDDIR»/resolver-b0HCFz/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 ... 25%
(Reading database ... 30%
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(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 ... 12076 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 ... 12093 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-llH8qF/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-LrJ787/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,77 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 10 not upgraded.
+Need to get 20.5 MB/20.5 MB of archives.
+After this operation, 78.0 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-LrJ787/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 http://ftp.uk.debian.org/debian unstable/main mipsel bash-completion all 1:2.1-4.2 [179 kB]
+Get:3 http://ftp.uk.debian.org/debian unstable/main mipsel groff-base mipsel 1.22.3-7 [1281 kB]
+Get:4 http://ftp.uk.debian.org/debian unstable/main mipsel bsdmainutils mipsel 9.0.6+b1 [185 kB]
+Get:5 http://ftp.uk.debian.org/debian unstable/main mipsel libpipeline1 mipsel 1.4.1-2 [27.3 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/main mipsel man-db mipsel 2.7.5-1 [991 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/main mipsel autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main mipsel libsigsegv2 mipsel 2.10-4+b1 [29.0 kB]
+Get:9 http://ftp.uk.debian.org/debian unstable/main mipsel libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
+Get:10 http://ftp.uk.debian.org/debian unstable/main mipsel libmagic1 mipsel 1:5.25-2 [258 kB]
+Get:11 http://ftp.uk.debian.org/debian unstable/main mipsel file mipsel 1:5.25-2 [61.6 kB]
+Get:12 http://ftp.uk.debian.org/debian unstable/main mipsel gettext-base mipsel 0.19.7-2 [114 kB]
+Get:13 http://ftp.uk.debian.org/debian unstable/main mipsel libicu55 mipsel 55.1-7 [7586 kB]
+Get:14 http://ftp.uk.debian.org/debian unstable/main mipsel libxml2 mipsel 2.9.3+dfsg1-1 [829 kB]
+Get:15 http://ftp.uk.debian.org/debian unstable/main mipsel m4 mipsel 1.4.17-5 [249 kB]
+Get:16 http://ftp.uk.debian.org/debian unstable/main mipsel autoconf all 2.69-9 [338 kB]
+Get:17 http://ftp.uk.debian.org/debian unstable/main mipsel autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://ftp.uk.debian.org/debian unstable/main mipsel automake all 1:1.15-3 [735 kB]
+Get:19 http://ftp.uk.debian.org/debian unstable/main mipsel libffi6 mipsel 3.2.1-4 [18.6 kB]
+Get:20 http://ftp.uk.debian.org/debian unstable/main mipsel libglib2.0-0 mipsel 2.46.2-3 [2501 kB]
+Get:21 http://ftp.uk.debian.org/debian unstable/main mipsel libcroco3 mipsel 0.6.11-1 [131 kB]
+Get:22 http://ftp.uk.debian.org/debian unstable/main mipsel gettext mipsel 0.19.7-2 [1451 kB]
+Get:23 http://ftp.uk.debian.org/debian unstable/main mipsel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://ftp.uk.debian.org/debian unstable/main mipsel po-debconf all 1.0.19 [249 kB]
+Get:25 http://ftp.uk.debian.org/debian unstable/main mipsel libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://ftp.uk.debian.org/debian unstable/main mipsel libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://ftp.uk.debian.org/debian unstable/main mipsel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://ftp.uk.debian.org/debian unstable/main mipsel dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://ftp.uk.debian.org/debian unstable/main mipsel debhelper all 9.20160115 [827 kB]
+Get:30 http://ftp.uk.debian.org/debian unstable/main mipsel libhts1 mipsel 1.3-1 [229 kB]
+Get:31 http://ftp.uk.debian.org/debian unstable/main mipsel libhts-dev mipsel 1.3-1 [319 kB]
+Get:32 http://ftp.uk.debian.org/debian unstable/main mipsel libio-pty-perl mipsel 1:1.08-1.1+b1 [31.5 kB]
+Get:33 http://ftp.uk.debian.org/debian unstable/main mipsel libtinfo-dev mipsel 6.0+20151024-2 [78.8 kB]
+Get:34 http://ftp.uk.debian.org/debian unstable/main mipsel libncurses5-dev mipsel 6.0+20151024-2 [177 kB]
+Get:35 http://ftp.uk.debian.org/debian unstable/main mipsel tabix mipsel 1.3-1 [231 kB]
+Get:36 http://ftp.uk.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 18.3 MB in 1s (10.0 MB/s)
+Fetched 20.5 MB in 2s (9861 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 ... 12076 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 ... 12093 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_1.22.3-4_mipsel.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_mipsel.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_mipsel.deb ...
+Unpacking libpipeline1:mipsel (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_mipsel.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:mipsel.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_mipsel.deb ...
+Unpacking libsigsegv2:mipsel (2.10-4+b1) ...
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) ...
@@ -223,53 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_mipsel.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:mipsel.
-Preparing to unpack .../libicu55_55.1-6_mipsel.deb ...
-Unpacking libicu55:mipsel (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_mipsel.deb ...
+Unpacking libicu55:mipsel (55.1-7) ...
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 m4.
+Preparing to unpack .../m4_1.4.17-5_mipsel.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_mipsel.deb ...
+Unpacking libglib2.0-0:mipsel (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_mipsel.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:mipsel.
-Preparing to unpack .../libhts1_1.2.1-2_mipsel.deb ...
-Unpacking libhts1:mipsel (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_mipsel.deb ...
+Unpacking libhts1:mipsel (1.3-1) ...
Selecting previously unselected package libhts-dev:mipsel.
-Preparing to unpack .../libhts-dev_1.2.1-2_mipsel.deb ...
-Unpacking libhts-dev:mipsel (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_mipsel.deb ...
+Unpacking libhts-dev:mipsel (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_mipsel.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -280,59 +306,66 @@ Selecting previously unselected package libncurses5-dev:mipsel.
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_1.2.1-2_mipsel.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../tabix_1.3-1_mipsel.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:mipsel (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:mipsel (2.10-4+b1) ...
Setting up libunistring0:mipsel (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:mipsel (55.1-7) ...
Setting up libxml2:mipsel (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:mipsel (3.2.1-4) ...
-Setting up libglib2.0-0:mipsel (2.46.2-1) ...
+Setting up libglib2.0-0:mipsel (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:mipsel (1.3-1) ...
+Setting up libhts-dev:mipsel (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
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_2.25.90.20151209-1 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 [...]
+Kernel: Linux 3.16.0-4-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,36 +403,43 @@ SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mipsel-sbuild-9e652671-aee1-4cf5-8e07-388c5b6c3a4d
+SCHROOT_SESSION_ID=sid-mipsel-sbuild-ab539df7-da35-49a8-9d8f-c2d942ce0cc8
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-USERNAME=buildd
-XDG_SESSION_ID=c112
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=c2910
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture mipsel
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j5 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j5 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -422,189 +461,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=mipsel-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/mipsel-linux-gnu --libexecdir=\${prefix}/lib/mipsel-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j5 HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j5 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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_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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
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/mipsel-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j5 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j5 test 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/NhyY4wH34k/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/0l8Ujf59YU/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/0l8Ujf59YU/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/0l8Ujf59YU/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/NhyY4wH34k/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/NhyY4wH34k/bgzip.dat.gz
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 1:100-104 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa 1:99998-100007 | grep -v '^>'
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/0l8Ujf59YU/dict.fa.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/NhyY4wH34k/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/NhyY4wH34k/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/0l8Ujf59YU/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/NhyY4wH34k/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/0l8Ujf59YU/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/0l8Ujf59YU/large_chrom.bam ref2:1-541556283
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/NhyY4wH34k/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/NhyY4wH34k/mpileup.bam.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/0l8Ujf59YU/mpileup.bam.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/0l8Ujf59YU/mpileup.bam.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/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/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/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/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/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/NhyY4wH34k/mpileup.cram.list -f /tmp/NhyY4wH34k/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/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:1050-1060 /tmp/0l8Ujf59YU/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:1050-1060 /tmp/0l8Ujf59YU/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -643,7 +737,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -673,7 +771,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -690,9 +796,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -724,6 +828,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -826,83 +934,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/NhyY4wH34k/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/NhyY4wH34k/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/NhyY4wH34k/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/NhyY4wH34k/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/NhyY4wH34k/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/NhyY4wH34k/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input).. ok
- 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
+ 67: Filter -l Library 2 (SAM input) .. ok
- 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
+ 68: Count -l Library 2 (SAM input) .. ok
+ 69: Filter -l Library 2 (BAM input) .. ok
-.. expected failure
-
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
- 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
+ 71: Filter -l Library 2 (CRAM input) .. ok
-
-.. expected failure
-
- 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
-
- 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
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1322,132 +1400,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
+
+ 6: cat CRAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 7: cat BAM files with new header .. ok
- 5: cat BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1459,12 +1542,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/BGs1KDNSoU - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/PzR_6A1_7E - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1487,381 +1600,106 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
-Number of tests:
- total .. 368
- passed .. 336
- failed .. 0
- expected failure .. 32
- unexpected pass .. 0
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
-test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
-test/merge/test_rtrans_build
-test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-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}'
-
-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/mipsel-linux-gnu/libhts.a
- install -d debian/samtools
- make -j5 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-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
-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/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/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}
- 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_mipsel.deb'.
- dpkg-deb --build debian/samtools ..
-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 20151221-1337
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
-Finished
-────────
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
-I: Built successfully
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build Chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
-samtools_1.2-4_mipsel.changes:
-──────────────────────────────
+ ERR:
+.. failed ...
-Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
-Source: samtools
-Binary: samtools samtools-test
-Architecture: mipsel
-Version: 1.2-4
-Distribution: sid
-Urgency: medium
-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: 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:
- e6dd76cf045f7ade59e4d44614e6b799586176d7 409544 samtools-dbgsym_1.2-4_mipsel.deb
- 8ac85d4a56b4f135c0a4c5d13774bc71302ce917 378468 samtools_1.2-4_mipsel.deb
-Checksums-Sha256:
- 79dcedf7107e7e78edf4e260f6a6243b9a17e25a89544a196fd14d9a7dbc70ea 409544 samtools-dbgsym_1.2-4_mipsel.deb
- 7197de1611a41506f56ebfe2cd2f4f0ad1fec52e76b864ea420369e3bafcf1ab 378468 samtools_1.2-4_mipsel.deb
-Files:
- c75f46e25c5611eea273ea399b7736ca 409544 debug extra samtools-dbgsym_1.2-4_mipsel.deb
- 227df3c390afe5dc1f5e92b240ef98e1 378468 science optional samtools_1.2-4_mipsel.deb
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
+ ERR:
+.. failed ...
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
-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 378468 bytes: control archive=1612 bytes.
- 809 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
- Package: samtools
- Version: 1.2-4
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1153
- Depends: libc6 (>= 2.15), 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 2015-12-21 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 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 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 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 2015-12-21 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 2015-12-21 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
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+
+Number of tests:
+ total .. 416
+ passed .. 396
+ failed .. 2
+ expected failure .. 18
+ unexpected pass .. 0
+
+Makefile:201: recipe for target 'test' failed
+make[2]: *** [test] Error 1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+dh_auto_test: make -j5 test BGZIP=/usr/bin/bgzip returned exit code 2
+debian/rules:25: recipe for target 'override_dh_auto_test' failed
+make[1]: *** [override_dh_auto_test] Error 2
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+debian/rules:6: recipe for target 'build-arch' failed
+make: *** [build-arch] Error 2
+dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20160205-1730
+
+Finished
+────────
+
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1875,23 +1713,20 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mipsel
-Build-Space: 19908
-Build-Time: 724
+Build-Space: 23920
+Build-Time: 401
Distribution: sid
+Fail-Stage: build
Host Architecture: mipsel
-Install-Time: 71
-Job: samtools_1.2-4
+Install-Time: 69
+Job: samtools_1.3-1
Machine Architecture: mipsel
Package: samtools
-Package-Time: 877
-Source-Version: 1.2-4
-Space: 19908
-Status: successful
-Version: 1.2-4
+Package-Time: 565
+Source-Version: 1.3-1
+Space: 23920
+Status: attempted
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160205-1730
+Build needed 00:09:25, 23920k disc space
diff --git a/powerpcspe.log b/powerpcspe.log
new file mode 100644
index 0000000..76f6c00
--- /dev/null
+++ b/powerpcspe.log
@@ -0,0 +1,795 @@
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on atlantis.physik.fu-berlin.de
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.3-1 (powerpcspe) 30 Mar 2016 22:47 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.3-1
+Source Version: 1.3-1
+Distribution: sid
+Machine Architecture: powerpcspe
+Host Architecture: powerpcspe
+Build Architecture: powerpcspe
+
+I: NOTICE: Log filtering will replace 'build/samtools-wui7wT/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-wui7wT' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-powerpcspe-sbuild-3c977843-6c1a-4b2a-a020-34cfe5c56370' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Hit http://ftp.de.debian.org unstable InRelease
+Hit http://ftp.de.debian.org unreleased InRelease
+Hit http://ftp.debian.org unstable InRelease
+Hit http://incoming.debian.org buildd-unstable InRelease
+Hit http://ftp.de.debian.org unstable/main powerpcspe Packages
+Ign http://incoming.debian-ports.org unstable InRelease
+Hit http://ftp.de.debian.org unreleased/main powerpcspe Packages
+Ign http://ftp.de.debian.org unstable/main Translation-en
+Ign http://ftp.de.debian.org unreleased/main Translation-en
+Hit http://incoming.debian-ports.org unstable Release.gpg
+Hit http://incoming.debian-ports.org unstable Release
+Get:1 http://ftp.debian.org unstable/main Sources/DiffIndex [16.1 kB]
+Hit http://incoming.debian.org buildd-unstable/main Sources
+Hit http://incoming.debian-ports.org unstable/main powerpcspe Packages
+Ign http://incoming.debian-ports.org unstable/main Translation-en
+Fetched 16.1 kB in 5s (2747 B/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ 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:
+https://anonscm.debian.org/git/debian-med/samtools.git
+Need to get 3757 kB of source archives.
+Get:1 http://ftp.debian.org/debian/ unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://ftp.debian.org/debian/ unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://ftp.debian.org/debian/ unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 0s (4647 kB/s)
+Download complete and in download only mode
+
+Check architectures
+───────────────────
+
+
+Check dependencies
+──────────────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-69Y3hJ/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+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 64 not upgraded.
+Need to get 0 B/766 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(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 ... 38197 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-P9VVTu/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ autoconf-archive bash-completion libhts-dev libhts1 libio-pty-perl tabix
+The following NEW packages will be installed:
+ autoconf-archive bash-completion libhts-dev libhts1 libio-pty-perl
+ sbuild-build-depends-samtools-dummy tabix
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 7 newly installed, 0 to remove and 64 not upgraded.
+Need to get 0 B/1622 kB of archives.
+After this operation, 10.1 MB of additional disk space will be used.
+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 ... 38197 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 autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libhts1:powerpcspe.
+Preparing to unpack .../libhts1_1.3-2_powerpcspe.deb ...
+Unpacking libhts1:powerpcspe (1.3-2) ...
+Selecting previously unselected package libhts-dev:powerpcspe.
+Preparing to unpack .../libhts-dev_1.3-2_powerpcspe.deb ...
+Unpacking libhts-dev:powerpcspe (1.3-2) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1_powerpcspe.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.3-2_powerpcspe.deb ...
+Unpacking tabix (1.3-2) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for man-db (2.7.5-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Processing triggers for libc-bin (2.22-3) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up autoconf-archive (20150925-1) ...
+Setting up libhts1:powerpcspe (1.3-2) ...
+Setting up libhts-dev:powerpcspe (1.3-2) ...
+Setting up libio-pty-perl (1:1.08-1.1) ...
+Setting up tabix (1.3-2) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.22-3) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.12.19-rt30_Daz_Tabor_04 powerpcspe (ppc)
+Toolchain package versions: binutils_2.26-4 dpkg-dev_1.18.4 g++-4.9_4.9.2-10 g++-5_5.3.1-11+b1 gcc-4.9_4.9.2-10 gcc-5_5.3.1-11+b1 libc6-dev_2.22-3 libstdc++-4.9-dev_4.9.2-10 libstdc++-5-dev_5.3.1-11+b1 libstdc++6_5.3.1-11+b1 linux-libc-dev_3.16.7-ckt9-3
+Package versions: acl_2.2.52-3 adduser_3.114 apt_1.0.9.9 autoconf_2.69-9 autoconf-archive_20150925-1 autoconf2.64_2.64+dfsg-0.1 autogen_1:5.18.7-3 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.37 bash_4.3-12 bash-completion_1:2.1-4.2 binutils_2.26-4 bison_2:3.0.4.dfsg-1 bsdmainutils_9.0.8 bsdutils_1:2.27.1-6 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 chrpath_0.16-1 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-4.9_4.9.2-10 cpp-5_5.3.1- [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
+dpkg-source: info: applying mayhem.patch
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=nobench nocheck parallel=4
+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-powerpcspe-sbuild
+SCHROOT_CHROOT_NAME=sid-powerpcspe-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=125
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-powerpcspe-sbuild-3c977843-6c1a-4b2a-a020-34cfe5c56370
+SCHROOT_UID=117
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_SESSION_ID=c3097
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.3
+dpkg-buildpackage: host architecture powerpcspe
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ debian/rules override_dh_auto_clean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+dh_auto_clean --
+ make -j4 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
+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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
+rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -rf debian/.debhelper/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=powerpc-linux-gnuspe --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/powerpc-linux-gnuspe --libexecdir=\${prefix}/lib/powerpc-linux-gnuspe --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ BGZIP=/usr/bin/bgzip
+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
+ install -d debian/samtools
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
+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 misc/wgsim.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 test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
+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_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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
+ dh_installman -a -O--parallel
+ 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 -a -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/NEWS.Debian 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/NEWS.Debian 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/powerpc-linux-gnuspe/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/dbgsym-root/usr/lib/debug/.build-id/e4
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/772eed8c0254f1b7218e7e6e2c9f88fe248a2d.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/772eed8c0254f1b7218e7e6e2c9f88fe248a2d.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e4/772eed8c0254f1b7218e7e6e2c9f88fe248a2d.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/799f374ce25d3b99aa61bd1135feda9eee683e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/799f374ce25d3b99aa61bd1135feda9eee683e.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/799f374ce25d3b99aa61bd1135feda9eee683e.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/4d37a21b99a8bc5eba1f3c77c615baca3cb366.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/4d37a21b99a8bc5eba1f3c77c615baca3cb366.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/4d37a21b99a8bc5eba1f3c77c615baca3cb366.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/4f8475c280945a53857182a88b910c36a7fb18.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/4f8475c280945a53857182a88b910c36a7fb18.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/71/4f8475c280945a53857182a88b910c36a7fb18.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f9/06eed21a0d5f73fb8392faee4aebb1446eebef.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f9/06eed21a0d5f73fb8392faee4aebb1446eebef.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f9/06eed21a0d5f73fb8392faee4aebb1446eebef.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/30ffcb63f046544e44ffef35ece49dfaca42d4.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/30ffcb63f046544e44ffef35ece49dfaca42d4.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/65/30ffcb63f046544e44ffef35ece49dfaca42d4.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/eb94d3c5d7fa08774cfed87c6f913bcc63fd96.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/eb94d3c5d7fa08774cfed87c6f913bcc63fd96.debug
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/eb94d3c5d7fa08774cfed87c6f913bcc63fd96.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam
+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/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa were not linked against libdl.so.2 (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/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=6530ffcb63f046544e44ffef35ece49dfaca42d4 714f8475c280945a53857182a88b910c36a7fb18 724d37a21b99a8bc5eba1f3c77c615ba [...]
+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/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 ${perl:Depends}
+ chmod 0644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_powerpcspe.deb'.
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.3-1_powerpcspe.deb'.
+ dpkg-genchanges -B -mDebian/powerpcspe buildd <buildd_powerpcspe-atlantis at glaubitz.dialup.fu-berlin.de> >../samtools_1.3-1_powerpcspe.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-buildpackage: binary-only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20160330-2251
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.3-1_powerpcspe.changes:
+──────────────────────────────────
+
+Format: 1.8
+Date: Fri, 05 Feb 2016 08:32:40 +0000
+Source: samtools
+Binary: samtools samtools-test
+Architecture: powerpcspe
+Version: 1.3-1
+Distribution: sid
+Urgency: medium
+Maintainer: Debian/powerpcspe buildd <buildd_powerpcspe-atlantis at glaubitz.dialup.fu-berlin.de>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Changes:
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
+ .
+ [ Sascha Steinbiss ]
+ * Team upload
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
+ * Fix spelling
+Checksums-Sha1:
+ 90bfc0422ce650b52a759b001e5ba23fe8b1ae18 464500 samtools-dbgsym_1.3-1_powerpcspe.deb
+ fe46019d52a6fa7276e8b40e401a10905458a1c2 240900 samtools_1.3-1_powerpcspe.deb
+Checksums-Sha256:
+ 1b47a0f9826b7509da52a3c32c516a6b28589b65f0bd628e5c6c90edd37bdbca 464500 samtools-dbgsym_1.3-1_powerpcspe.deb
+ 96965abbb277fe3878c8d2b204d48d044236427622a06f6b117c512ec2352bd3 240900 samtools_1.3-1_powerpcspe.deb
+Files:
+ 270850a7aa1adb4d2a51d19852f4291d 464500 debug extra samtools-dbgsym_1.3-1_powerpcspe.deb
+ 4c5a0a920f1a2d6d0c37b99547e6292a 240900 science optional samtools_1.3-1_powerpcspe.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-dbgsym_1.3-1_powerpcspe.deb
+────────────────────────────────────
+
+ new debian package, version 2.0.
+ size 464500 bytes: control archive=823 bytes.
+ 651 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.3-1
+ Architecture: powerpcspe
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 519
+ Depends: samtools (= 1.3-1)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 6530ffcb63f046544e44ffef35ece49dfaca42d4 714f8475c280945a53857182a88b910c36a7fb18 724d37a21b99a8bc5eba1f3c77c615baca3cb366 a9eb94d3c5d7fa08774cfed87c6f913bcc63fd96 d1799f374ce25d3b99aa61bd1135feda9eee683e e4772eed8c0254f1b7218e7e6e2c9f88fe248a2d f906eed21a0d5f73fb8392faee4aebb1446eebef
+
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/65/
+-rw-r--r-- root/root 10280 2016-03-30 22:51 ./usr/lib/debug/.build-id/65/30ffcb63f046544e44ffef35ece49dfaca42d4.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/71/
+-rw-r--r-- root/root 7220 2016-03-30 22:51 ./usr/lib/debug/.build-id/71/4f8475c280945a53857182a88b910c36a7fb18.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/72/
+-rw-r--r-- root/root 435060 2016-03-30 22:51 ./usr/lib/debug/.build-id/72/4d37a21b99a8bc5eba1f3c77c615baca3cb366.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/a9/
+-rw-r--r-- root/root 18704 2016-03-30 22:51 ./usr/lib/debug/.build-id/a9/eb94d3c5d7fa08774cfed87c6f913bcc63fd96.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/d1/
+-rw-r--r-- root/root 10012 2016-03-30 22:51 ./usr/lib/debug/.build-id/d1/799f374ce25d3b99aa61bd1135feda9eee683e.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/e4/
+-rw-r--r-- root/root 18768 2016-03-30 22:51 ./usr/lib/debug/.build-id/e4/772eed8c0254f1b7218e7e6e2c9f88fe248a2d.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/lib/debug/.build-id/f9/
+-rw-r--r-- root/root 10280 2016-03-30 22:51 ./usr/lib/debug/.build-id/f9/06eed21a0d5f73fb8392faee4aebb1446eebef.debug
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-03-30 22:51 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_powerpcspe.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 240900 bytes: control archive=1635 bytes.
+ 812 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
+ Package: samtools
+ Version: 1.3-1
+ Architecture: powerpcspe
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1052
+ Depends: libc6 (>= 2.7), libhts1 (>= 1.3), 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 2016-03-30 22:51 ./
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/bin/
+-rwxr-xr-x root/root 67084 2016-03-30 22:51 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 67072 2016-03-30 22:51 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 67072 2016-03-30 22:51 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 67004 2016-03-30 22:51 ./usr/bin/md5fa
+-rwxr-xr-x root/root 66968 2016-03-30 22:51 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 461464 2016-03-30 22:51 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 67232 2016-03-30 22:51 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-03-30 22:51 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-03-30 22:51 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-03-30 22:51 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-03-30 22:51 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-03-30 22:51 ./usr/share/man/man1/wgsim.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 64 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ autoconf-archive* bash-completion* libhts-dev* libhts1* libio-pty-perl*
+ sbuild-build-depends-core-dummy* sbuild-build-depends-samtools-dummy* tabix*
+0 upgraded, 0 newly installed, 8 to remove and 64 not upgraded.
+After this operation, 10.1 MB disk space will be freed.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 39950 files and directories currently installed.)
+Removing sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Removing autoconf-archive (20150925-1) ...
+Purging configuration files for autoconf-archive (20150925-1) ...
+Removing bash-completion (1:2.1-4.2) ...
+Purging configuration files for bash-completion (1:2.1-4.2) ...
+Removing libhts-dev:powerpcspe (1.3-2) ...
+Removing libhts1:powerpcspe (1.3-2) ...
+Removing libio-pty-perl (1:1.08-1.1) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing tabix (1.3-2) ...
+Processing triggers for man-db (2.7.5-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Processing triggers for libc-bin (2.22-3) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: powerpcspe
+Build-Space: 16816
+Build-Time: 203
+Distribution: sid
+Host Architecture: powerpcspe
+Install-Time: 37
+Job: samtools_1.3-1
+Machine Architecture: powerpcspe
+Package: samtools
+Package-Time: 265
+Source-Version: 1.3-1
+Space: 16816
+Status: successful
+Version: 1.3-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20160330-2251
+Build needed 00:04:25, 16816k disc space
+Signature with key '905E537D' requested:
+ signfile /var/lib/buildd/build/samtools_1.3-1_powerpcspe.changes 905E537D
+
+Successfully signed changes file
diff --git a/ppc64el.log b/ppc64el.log
index 5496f9a..0e9c674 100644
--- a/ppc64el.log
+++ b/ppc64el.log
@@ -2,44 +2,44 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on ppc64el-osuosl-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (ppc64el) 21 Dec 2015 14:40 ║
+║ samtools 1.3-1 (ppc64el) 05 Feb 2016 16:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: ppc64el
Host Architecture: ppc64el
Build Architecture: ppc64el
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-pvdtn1/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-pvdtn1' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-86091641-d380-44ba-8303-2e9b0d56163f' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://debian.osuosl.org/debian unstable InRelease [278 kB]
+Get:2 http://debian.osuosl.org/debian unstable/main Sources [8513 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:5 http://debian.osuosl.org/debian unstable/contrib Sources [61.4 kB]
+Get:6 http://debian.osuosl.org/debian unstable/non-free Sources [106 kB]
+Get:7 http://debian.osuosl.org/debian unstable/main ppc64el Packages [7830 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Get:9 http://debian.osuosl.org/debian unstable/contrib ppc64el Packages [44.9 kB]
+Get:10 http://ftp.debian.org/debian unstable/main Sources [8513 kB]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [4284 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [1736 B]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/main ppc64el Packages [175 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib ppc64el Packages [1108 B]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [61.4 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [106 kB]
+Get:17 http://ftp.debian.org/debian unstable/main ppc64el Packages [7830 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib ppc64el Packages [44.9 kB]
+Fetched 34.1 MB in 6s (4887 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -60,15 +60,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 1s (2100 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +82,16 @@ 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-BtwcEv/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-uhfl1o/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-uhfl1o/apt_archive ./ Packages [526 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +106,29 @@ Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
-0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
-Need to get 0 B/770 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 10 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-BtwcEv/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-uhfl1o/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 ...
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(Reading database ... 75%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12151 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 12166 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-mIjJWx/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 4:5.3), g++ (>= 4:5.3), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-wxdTHW/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ Packages [746 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,77 +142,91 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 man-db po-debconf
+ tabix zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool 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
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev 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 libsigsegv2
+ libtimedate-perl libtinfo-dev libunistring0 libxml2 m4 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]
+0 upgraded, 36 newly installed, 0 to remove and 10 not upgraded.
+Need to get 20.4 MB/20.4 MB of archives.
+After this operation, 82.1 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-wxdTHW/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [992 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:3 http://debian.osuosl.org/debian unstable/main ppc64el groff-base ppc64el 1.22.3-7 [1229 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:5 http://debian.osuosl.org/debian unstable/main ppc64el libpipeline1 ppc64el 1.4.1-2 [26.6 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]
+Get:7 http://debian.osuosl.org/debian unstable/main ppc64el autoconf-archive all 20150925-1 [688 kB]
+Get:8 http://debian.osuosl.org/debian unstable/main ppc64el libsigsegv2 ppc64el 2.10-4+b1 [29.0 kB]
+Get:9 http://debian.osuosl.org/debian unstable/main ppc64el libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
+Get:10 http://debian.osuosl.org/debian unstable/main ppc64el libmagic1 ppc64el 1:5.25-2 [253 kB]
+Get:11 http://debian.osuosl.org/debian unstable/main ppc64el file ppc64el 1:5.25-2 [61.7 kB]
+Get:12 http://debian.osuosl.org/debian unstable/main ppc64el gettext-base ppc64el 0.19.7-2 [113 kB]
+Get:13 http://debian.osuosl.org/debian unstable/main ppc64el libicu55 ppc64el 55.1-7 [7626 kB]
+Get:14 http://debian.osuosl.org/debian unstable/main ppc64el libxml2 ppc64el 2.9.3+dfsg1-1 [830 kB]
+Get:15 http://debian.osuosl.org/debian unstable/main ppc64el m4 ppc64el 1.4.17-5 [248 kB]
+Get:16 http://debian.osuosl.org/debian unstable/main ppc64el autoconf all 2.69-9 [338 kB]
+Get:17 http://debian.osuosl.org/debian unstable/main ppc64el autotools-dev all 20150820.1 [71.7 kB]
+Get:18 http://debian.osuosl.org/debian unstable/main ppc64el automake all 1:1.15-3 [735 kB]
+Get:19 http://debian.osuosl.org/debian unstable/main ppc64el libffi6 ppc64el 3.2.1-4 [20.5 kB]
+Get:20 http://debian.osuosl.org/debian unstable/main ppc64el libglib2.0-0 ppc64el 2.46.2-3 [2503 kB]
+Get:21 http://debian.osuosl.org/debian unstable/main ppc64el libcroco3 ppc64el 0.6.11-1 [133 kB]
+Get:22 http://debian.osuosl.org/debian unstable/main ppc64el gettext ppc64el 0.19.7-2 [1430 kB]
+Get:23 http://debian.osuosl.org/debian unstable/main ppc64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:24 http://debian.osuosl.org/debian unstable/main ppc64el po-debconf all 1.0.19 [249 kB]
+Get:25 http://debian.osuosl.org/debian unstable/main ppc64el libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:26 http://debian.osuosl.org/debian unstable/main ppc64el libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:27 http://debian.osuosl.org/debian unstable/main ppc64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:28 http://debian.osuosl.org/debian unstable/main ppc64el dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:29 http://debian.osuosl.org/debian unstable/main ppc64el debhelper all 9.20160115 [827 kB]
+Get:30 http://debian.osuosl.org/debian unstable/main ppc64el libhts1 ppc64el 1.3-1 [227 kB]
+Get:31 http://debian.osuosl.org/debian unstable/main ppc64el libhts-dev ppc64el 1.3-1 [295 kB]
+Get:32 http://debian.osuosl.org/debian unstable/main ppc64el libio-pty-perl ppc64el 1:1.08-1.1+b1 [33.0 kB]
+Get:33 http://debian.osuosl.org/debian unstable/main ppc64el libtinfo-dev ppc64el 6.0+20151024-2 [77.6 kB]
+Get:34 http://debian.osuosl.org/debian unstable/main ppc64el libncurses5-dev ppc64el 6.0+20151024-2 [175 kB]
+Get:35 http://debian.osuosl.org/debian unstable/main ppc64el tabix ppc64el 1.3-1 [216 kB]
+Get:36 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 18.3 MB in 0s (20.6 MB/s)
+Fetched 20.4 MB in 1s (16.3 MB/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 ... 12151 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 ... 12166 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_1.22.3-4_ppc64el.deb ...
-Unpacking groff-base (1.22.3-4) ...
+Preparing to unpack .../groff-base_1.22.3-7_ppc64el.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
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) ...
+Preparing to unpack .../libpipeline1_1.4.1-2_ppc64el.deb ...
+Unpacking libpipeline1:ppc64el (1.4.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../man-db_2.7.5-1_ppc64el.deb ...
Unpacking man-db (2.7.5-1) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:ppc64el.
+Preparing to unpack .../libsigsegv2_2.10-4+b1_ppc64el.deb ...
+Unpacking libsigsegv2:ppc64el (2.10-4+b1) ...
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) ...
@@ -223,53 +237,65 @@ Selecting previously unselected package file.
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) ...
+Preparing to unpack .../gettext-base_0.19.7-2_ppc64el.deb ...
+Unpacking gettext-base (0.19.7-2) ...
Selecting previously unselected package libicu55:ppc64el.
-Preparing to unpack .../libicu55_55.1-6_ppc64el.deb ...
-Unpacking libicu55:ppc64el (55.1-6) ...
+Preparing to unpack .../libicu55_55.1-7_ppc64el.deb ...
+Unpacking libicu55:ppc64el (55.1-7) ...
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 m4.
+Preparing to unpack .../m4_1.4.17-5_ppc64el.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.46.2-3_ppc64el.deb ...
+Unpacking libglib2.0-0:ppc64el (2.46.2-3) ...
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) ...
+Preparing to unpack .../gettext_0.19.7-2_ppc64el.deb ...
+Unpacking gettext (0.19.7-2) ...
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_1.55-1_all.deb ...
-Unpacking libarchive-zip-perl (1.55-1) ...
+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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:ppc64el.
-Preparing to unpack .../libhts1_1.2.1-2_ppc64el.deb ...
-Unpacking libhts1:ppc64el (1.2.1-2) ...
+Preparing to unpack .../libhts1_1.3-1_ppc64el.deb ...
+Unpacking libhts1:ppc64el (1.3-1) ...
Selecting previously unselected package libhts-dev:ppc64el.
-Preparing to unpack .../libhts-dev_1.2.1-2_ppc64el.deb ...
-Unpacking libhts-dev:ppc64el (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_ppc64el.deb ...
+Unpacking libhts-dev:ppc64el (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_ppc64el.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -280,50 +306,57 @@ Selecting previously unselected package libncurses5-dev:ppc64el.
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_1.2.1-2_ppc64el.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../tabix_1.3-1_ppc64el.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-4) ...
+Setting up groff-base (1.22.3-7) ...
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 libpipeline1:ppc64el (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:ppc64el (2.10-4+b1) ...
Setting up libunistring0:ppc64el (0.9.3-5.2+b1) ...
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 gettext-base (0.19.7-2) ...
+Setting up libicu55:ppc64el (55.1-7) ...
Setting up libxml2:ppc64el (2.9.3+dfsg1-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libffi6:ppc64el (3.2.1-4) ...
-Setting up libglib2.0-0:ppc64el (2.46.2-1) ...
+Setting up libglib2.0-0:ppc64el (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:ppc64el (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up libarchive-zip-perl (1.55-1) ...
-Setting up libfile-stripnondeterminism-perl (0.014-1) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.56-2) ...
+Setting up libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:ppc64el (1.3-1) ...
+Setting up libhts-dev:ppc64el (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151220) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -331,8 +364,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.16.0-4-powerpc64le ppc64el (ppc64le)
-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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7+b1
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-strip-nondeterminism_0.01 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -343,15 +376,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -371,36 +403,43 @@ SCHROOT_CHROOT_NAME=sid-ppc64el-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ppc64el-sbuild-ab2c3439-7a90-4fba-9207-868f8c7627e8
+SCHROOT_SESSION_ID=sid-ppc64el-sbuild-86091641-d380-44ba-8303-2e9b0d56163f
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=1
+XDG_SESSION_ID=2
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture ppc64el
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j4 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j4 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -422,189 +461,244 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=powerpc64le-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/powerpc64le-linux-gnu --libexecdir=\${prefix}/lib/powerpc64le-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 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 -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.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 -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-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/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/powerpc64le-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/powerpc64le-linux-gnu/libhts.a -lhts -lcurses [...]
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
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/powerpc64le-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test 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/oWFXottKCB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/_Ps6Q96Nl9/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/oWFXottKCB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/_Ps6Q96Nl9/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/oWFXottKCB/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/_Ps6Q96Nl9/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/oWFXottKCB/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /«PKGBUILDDIR»/test/dat/dict.fa
+.. ok
+
+test_dict:
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/_Ps6Q96Nl9/dict.fa.gz
+.. ok
+
+test_dict:
+ cat /«PKGBUILDDIR»/test/dat/dict.fa | /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/oWFXottKCB/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/_Ps6Q96Nl9/large_chrom.bam
+ ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/oWFXottKCB/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/_Ps6Q96Nl9/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/oWFXottKCB/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/_Ps6Q96Nl9/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /«PKGBUILDDIR»/test/dat/test_input_1_a.bam && cat /«PKGBUILDDIR»/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/oWFXottKCB/mpileup.bam.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/_Ps6Q96Nl9/mpileup.bam.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/_Ps6Q96Nl9/mpileup.bam.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/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/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/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/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/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/oWFXottKCB/mpileup.cram.list -f /tmp/oWFXottKCB/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/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/_Ps6Q96Nl9/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/_Ps6Q96Nl9/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+ samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
+ samtools dict
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
@@ -643,7 +737,11 @@ test_usage_subcommand:
.. expected failure
test_usage_subcommand:
- samtools bamshuf
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
Usage on stderr rather than stdout
.. expected failure
@@ -673,7 +771,15 @@ test_usage_subcommand:
.. ok
test_usage_subcommand:
- samtools bam2fq
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
.. ok
test_usage_subcommand:
@@ -690,9 +796,7 @@ test_usage_subcommand:
test_usage_subcommand:
samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
+.. ok
test_usage_subcommand:
samtools idxstats
@@ -724,6 +828,10 @@ test_usage_subcommand:
test_usage_subcommand:
samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
Usage on stderr rather than stdout
.. expected failure
@@ -826,83 +934,53 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/oWFXottKCB/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/oWFXottKCB/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/oWFXottKCB/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/oWFXottKCB/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/oWFXottKCB/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/oWFXottKCB/view.001.fogn (CRAM input) .. ok
+ 49: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input) .. ok
- 55: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (SAM input).. ok
+ 50: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input) .. ok
- 56: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (SAM input).. ok
+ 51: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input) .. ok
- 57: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (BAM input).. ok
+ 52: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input) .. ok
- 58: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (BAM input).. ok
+ 53: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input) .. ok
- 59: Filter -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (CRAM input).. ok
+ 54: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input) .. ok
- 60: Count -R /tmp/oWFXottKCB/view.001.fogn -r grp2 (CRAM input).. ok
+ 55: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (SAM input).. ok
- 61: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (SAM input).. ok
+ 56: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (SAM input).. ok
- 62: Count -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (SAM input).. ok
+ 57: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (BAM input).. ok
- 63: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (BAM input).. ok
+ 58: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (BAM input).. ok
- 64: Count -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (BAM input).. ok
+ 59: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (CRAM input).. ok
- 65: Filter -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (CRAM input).. ok
+ 60: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/oWFXottKCB/view.001.fogn (CRAM input).. ok
+ 61: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input).. ok
- 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
+ 62: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input).. ok
+ 63: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
-
+ 64: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input).. ok
-.. expected failure
-
- 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
+ 65: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input).. ok
-.. expected failure
+ 67: Filter -l Library 2 (SAM input) .. ok
- 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
+ 68: Count -l Library 2 (SAM input) .. ok
+ 69: Filter -l Library 2 (BAM input) .. ok
-.. expected failure
-
- 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
+ 70: Count -l Library 2 (BAM input) .. ok
- 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
+ 71: Filter -l Library 2 (CRAM input) .. ok
-
-.. expected failure
+ 72: Count -l Library 2 (CRAM input) .. ok
73: Filter -q 50 (SAM input) .. ok
@@ -1322,132 +1400,137 @@ test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
+ Generate CRAM file #1 .. ok
+
Generating test data file .................. done
Generate BAM file #2 .. ok
+ Generate CRAM file #2 .. ok
+
Generating test data file .................. done
Generate BAM file #3 .. ok
+ Generate CRAM file #3 .. ok
+
Generating test data file .................. done
Generate BAM file #4 .. ok
+ Generate CRAM file #4 .. ok
+
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
- 3: cat BAM files to stdout .. ok
+ 3: cat CRAM files .. ok
+
+ 4: cat BAM files to stdout .. ok
+
+ 5: cat recompressed BAM files to stdout .. ok
- 4: cat recompressed BAM files to stdout .. ok
+ 6: cat CRAM files to stdout .. ok
- 5: cat BAM files with new header .. ok
+ 7: cat BAM files with new header .. ok
- 6: cat recompressed BAM files with new header .. ok
+ 8: cat recompressed BAM files with new header .. ok
+
+ 9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
- Generate CRAM file Unsorted mode enabled
-.. ok
+ Generate CRAM file .. ok
- 1: bam2fq (SAM input) [M::main_bam2fq] processed 36 reads
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 2: bam2fq -n (SAM input) [M::main_bam2fq] processed 36 reads
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 3: bam2fq (BAM input) [M::main_bam2fq] processed 36 reads
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 4: bam2fq -n (BAM input) [M::main_bam2fq] processed 36 reads
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 5: bam2fq (CRAM input) [M::main_bam2fq] processed 36 reads
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
- 6: bam2fq -n (CRAM input) [M::main_bam2fq] processed 36 reads
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
-test_depad:
- Generate BAM file .. ok
-
- 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
-
- 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
-
- 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
-
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
-.. expected failure
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.001.sam
+.. ok
- 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
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.002.sam
+.. ok
+test_bam2fq:
+ /«PKGBUILDDIR»/samtools fastq -s /«PKGBUILDDIR»/test/s.fq -1 /«PKGBUILDDIR»/test/1.fq -2 /«PKGBUILDDIR»/test/2.fq /«PKGBUILDDIR»/test/dat/bam2fq.003.sam
+.. ok
-.. expected failure
+test_depad:
+ Generate BAM file .. ok
- 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
+ depad (SAM input) .. ok
+ depad -s (SAM input) .. ok
-.. expected failure
+ depad -u (SAM input) .. ok
- 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
+ depad -1 (SAM input) .. ok
+ depad (BAM input) .. ok
-.. expected failure
+ depad -s (BAM input) .. ok
- 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
+ depad -u (BAM input) .. ok
+ depad -1 (BAM input) .. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
+.. ok
- 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
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
+.. ok
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
+.. ok
-.. expected failure
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+4
+.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+ /«PKGBUILDDIR»/samtools stats -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
@@ -1459,12 +1542,42 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/jBiMx9gPPd - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/3akp4iF0QF - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_b.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -r -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -cp -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a_regex.sam /«PKGBUILDDIR»/test/dat/test_input_1_b_regex.sam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sorttmp
.. ok
test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+ ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
+
.. expected failure
test_fixmate:
@@ -1487,24 +1600,91 @@ test_fixmate:
/«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/6_ct_replace.sam -
.. ok
+/«PKGBUILDDIR»/samtools calmd -uAr /«PKGBUILDDIR»/test/dat/mpileup.1.sam /«PKGBUILDDIR»/test/dat/mpileup.ref.fa
+.. ok
+
test_idxstat:
/«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam
+.. ok
+
+test_quickcheck:
+ /«PKGBUILDDIR»/samtools quickcheck -v /«PKGBUILDDIR»/test/quickcheck/1.quickcheck.badeof.bam /«PKGBUILDDIR»/test/quickcheck/2.quickcheck.badheader.bam /«PKGBUILDDIR»/test/quickcheck/3.quickcheck.ok.bam /«PKGBUILDDIR»/test/quickcheck/4.quickcheck.ok.bam | sed 's,.*/quickcheck/,,'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.bam | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | /«PKGBUILDDIR»/samtools view -h | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_reheader:
+ /«PKGBUILDDIR»/samtools reheader --in-place /«PKGBUILDDIR»/test/reheader/hdr.sam /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram && /«PKGBUILDDIR»/samtools view -h /«PKGBUILDDIR»/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m orphan_only /«PKGBUILDDIR»/test/addrprg/2_fixup_orphan.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -R '1#7' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
+.. ok
+
+test_addrprg:
+ /«PKGBUILDDIR»/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /«PKGBUILDDIR»/test/addrprg/4_fixup_norg.sam
+.. ok
+
Number of tests:
- total .. 368
- passed .. 336
+ total .. 416
+ passed .. 398
failed .. 0
- expected failure .. 32
+ expected failure .. 18
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
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}'
@@ -1514,6 +1694,15 @@ Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
+cd test/mpileup && ./regression.sh depth.reg
+
+=== Testing depth.reg regressions ===
+
+Expected passes: 14
+Unexpected passes: 0
+Expected failures: 0
+Unexpected failures: 0
+=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
@@ -1530,22 +1719,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -1567,16 +1755,17 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
@@ -1590,8 +1779,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -1607,59 +1796,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/07
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/07/2cfb7710feb6eb16337a2fa0155181351782cf.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/07/2cfb7710feb6eb16337a2fa0155181351782cf.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/07/2cfb7710feb6eb16337a2fa0155181351782cf.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/6e9f2ae4abeaaafd0d474241cad0a085ad52ce.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/6e9f2ae4abeaaafd0d474241cad0a085ad52ce.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/6e9f2ae4abeaaafd0d474241cad0a085ad52ce.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4e/c4ee49cb6d42cadda562d494034c22888a0604.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4e/c4ee49cb6d42cadda562d494034c22888a0604.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/4e/c4ee49cb6d42cadda562d494034c22888a0604.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/5111b1bccf342db0b9d46a4dcf33f794340a99.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/5111b1bccf342db0b9d46a4dcf33f794340a99.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/5111b1bccf342db0b9d46a4dcf33f794340a99.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d5
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d5/277349049173cd8b65410fb09e9c1650c278b5.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d5/277349049173cd8b65410fb09e9c1650c278b5.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d5/277349049173cd8b65410fb09e9c1650c278b5.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/21
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/21/e3c439df59b570c9c794ce4d073243c85e90ba.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/21/e3c439df59b570c9c794ce4d073243c85e90ba.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/21/e3c439df59b570c9c794ce4d073243c85e90ba.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/5318e9ca372729356fe0d64b913ecbe0431430.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/5318e9ca372729356fe0d64b913ecbe0431430.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/2a/5318e9ca372729356fe0d64b913ecbe0431430.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short 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 libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=026e9f2ae4abeaaafd0d474241cad0a085ad52ce 072cfb7710feb6eb16337a2fa0155181351782cf 21e3c439df59b570c9c794ce4d073243 [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -1669,22 +1858,22 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_ppc64el.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_ppc64el.deb'.
+ dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1444
+Build finished at 20160205-1637
Finished
────────
@@ -1701,108 +1890,108 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_ppc64el.changes:
+samtools_1.3-1_ppc64el.changes:
───────────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: ppc64el
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
Maintainer: ppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org>
-Changed-By: Andreas Tille <tille at debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- 30062220dbde816902edc104dfb4685a985475c8 415906 samtools-dbgsym_1.2-4_ppc64el.deb
- 39cbe3f009bc5fdd01fe895258ba362919b6d235 372672 samtools_1.2-4_ppc64el.deb
+ 3c3bed70b78b5fb18dca99a58ca4e0b495ae4561 468400 samtools-dbgsym_1.3-1_ppc64el.deb
+ eea1683836476a760df4ce3e89033479c0b4e449 236130 samtools_1.3-1_ppc64el.deb
Checksums-Sha256:
- 1394f1ff345a2b5d8832fd4ce9b132b858e346c2ed608542a4b0ca8785bb272a 415906 samtools-dbgsym_1.2-4_ppc64el.deb
- 251b43d66f98d66241da018f3bef1a1b5f09e28f4382b27e979a26f757269590 372672 samtools_1.2-4_ppc64el.deb
+ 5693b6d49d791bb301920185fd012a5b5aa890183e39daec8f6227a196457b9e 468400 samtools-dbgsym_1.3-1_ppc64el.deb
+ 56f69eb5e72679faf47b78c45ad0ed7388125b73ccdd51bf147676fc5425fce4 236130 samtools_1.3-1_ppc64el.deb
Files:
- bf292737b8481732b27cff9c70ed27c5 415906 debug extra samtools-dbgsym_1.2-4_ppc64el.deb
- 84f447214c80dec433960d465c3e562f 372672 science optional samtools_1.2-4_ppc64el.deb
+ 8e3ede7703e572b997654e0dbacca25f 468400 debug extra samtools-dbgsym_1.3-1_ppc64el.deb
+ 25b1b9f46928562ddad7fa59f9c459b9 236130 science optional samtools_1.3-1_ppc64el.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_ppc64el.deb
+samtools-dbgsym_1.3-1_ppc64el.deb
─────────────────────────────────
new debian package, version 2.0.
- size 415906 bytes: control archive=817 bytes.
+ size 468400 bytes: control archive=819 bytes.
648 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: ppc64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 514
- Depends: samtools (= 1.2-4)
+ Installed-Size: 553
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 026e9f2ae4abeaaafd0d474241cad0a085ad52ce 072cfb7710feb6eb16337a2fa0155181351782cf 21e3c439df59b570c9c794ce4d073243c85e90ba 2a5318e9ca372729356fe0d64b913ecbe0431430 4ec4ee49cb6d42cadda562d494034c22888a0604 d15111b1bccf342db0b9d46a4dcf33f794340a99 d5277349049173cd8b65410fb09e9c1650c278b5
+
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/02/
+-rw-r--r-- root/root 9640 2016-02-05 16:37 ./usr/lib/debug/.build-id/02/6e9f2ae4abeaaafd0d474241cad0a085ad52ce.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/07/
+-rw-r--r-- root/root 21840 2016-02-05 16:37 ./usr/lib/debug/.build-id/07/2cfb7710feb6eb16337a2fa0155181351782cf.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/21/
+-rw-r--r-- root/root 21448 2016-02-05 16:37 ./usr/lib/debug/.build-id/21/e3c439df59b570c9c794ce4d073243c85e90ba.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/2a/
+-rw-r--r-- root/root 455584 2016-02-05 16:37 ./usr/lib/debug/.build-id/2a/5318e9ca372729356fe0d64b913ecbe0431430.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/4e/
+-rw-r--r-- root/root 12872 2016-02-05 16:37 ./usr/lib/debug/.build-id/4e/c4ee49cb6d42cadda562d494034c22888a0604.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/d1/
+-rw-r--r-- root/root 13056 2016-02-05 16:37 ./usr/lib/debug/.build-id/d1/5111b1bccf342db0b9d46a4dcf33f794340a99.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/lib/debug/.build-id/d5/
+-rw-r--r-- root/root 13040 2016-02-05 16:37 ./usr/lib/debug/.build-id/d5/277349049173cd8b65410fb09e9c1650c278b5.debug
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-05 16:37 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_ppc64el.deb
──────────────────────────
new debian package, version 2.0.
- size 372672 bytes: control archive=1608 bytes.
+ size 236130 bytes: control archive=1634 bytes.
810 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: ppc64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1492
- Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 1060
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1815,47 +2004,48 @@ samtools_1.2-4_ppc64el.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/bin/
+-rwxr-xr-x root/root 67696 2016-02-05 16:37 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 21:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 21:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 21:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 21:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 67672 2016-02-05 16:37 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 67672 2016-02-05 16:37 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 67704 2016-02-05 16:37 ./usr/bin/md5fa
+-rwxr-xr-x root/root 67632 2016-02-05 16:37 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 21:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 21:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 21:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 21:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 462880 2016-02-05 16:37 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 21:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 21:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 21:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 21:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 67784 2016-02-05 16:37 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 21:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 21:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 21:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 14:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 14:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 14:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 14:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 14:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 14:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 16:37 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 16:37 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 16:37 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 16:37 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 16:37 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1875,23 +2065,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: ppc64el
-Build-Space: 37892
-Build-Time: 196
+Build-Space: 42548
+Build-Time: 200
Distribution: sid
Host Architecture: ppc64el
-Install-Time: 10
-Job: samtools_1.2-4
+Install-Time: 11
+Job: samtools_1.3-1
Machine Architecture: ppc64el
Package: samtools
-Package-Time: 230
-Source-Version: 1.2-4
-Space: 37892
+Package-Time: 229
+Source-Version: 1.3-1
+Space: 42548
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151221-1444
-Build needed 00:03:50, 37892k disc space
+Finished at 20160205-1637
+Build needed 00:03:49, 42548k disc space
Signature with key 'AE6C7FBC' requested:
- signfile /home/buildd/build/samtools_1.2-4_ppc64el.changes AE6C7FBC
+ signfile /home/buildd/build/samtools_1.3-1_ppc64el.changes AE6C7FBC
Successfully signed changes file
diff --git a/sh4.log b/sh4.log
index 0c011ef..5437aee 100644
--- a/sh4.log
+++ b/sh4.log
@@ -2,38 +2,55 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs95.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (sh4) 14 Jan 2016 16:38 ║
+║ samtools 1.3-1 (sh4) 06 Feb 2016 18:40 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: sh4
Build Architecture: sh4
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-TRMg5i/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-TRMg5i' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-sh4-sbuild-496666af-b742-41be-9ef6-535f3ec4abe5' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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]
+Ign:1 http://incoming.debian-ports.org/buildd unstable InRelease
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:3 http://incoming.debian-ports.org/buildd unstable Release [43.8 kB]
+Get:4 ftp://ftp.debian.org/debian unstable InRelease [287 kB]
+Get:5 http://incoming.debian-ports.org/buildd unstable Release.gpg [836 B]
+Get:6 ftp://ftp.debian-ports.org/debian unstable InRelease [37.1 kB]
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]
-Get:9 ftp://ftp.debian.org/debian unstable/main Sources [8469 kB]
-Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [272 kB]
-Get:11 http://incoming.debian-ports.org/buildd unstable/main sh4 Packages [54.2 kB]
-Get:12 ftp://ftp.debian-ports.org/debian unstable/main sh4 Packages [13.6 MB]
-Fetched 22.9 MB in 41s (551 kB/s)
+Get:9 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-02-2051.26.pdiff [12.3 kB]
+Get:10 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-0247.20.pdiff [7814 B]
+Get:11 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-0847.44.pdiff [5373 B]
+Get:12 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-1452.45.pdiff [20.5 kB]
+Get:13 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-03-2047.23.pdiff [15.1 kB]
+Get:14 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-0247.46.pdiff [26.0 kB]
+Get:15 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-0851.05.pdiff [14.2 kB]
+Get:16 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-1446.17.pdiff [14.1 kB]
+Get:17 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-04-2131.08.pdiff [18.5 kB]
+Get:18 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-0254.43.pdiff [5835 B]
+Get:19 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-0852.02.pdiff [8660 B]
+Get:20 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-1450.10.pdiff [29.4 kB]
+Get:21 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-05-2054.25.pdiff [13.1 kB]
+Get:22 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-06-0251.40.pdiff [13.8 kB]
+Get:23 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-06-0850.30.pdiff [2949 B]
+Get:24 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-06-1239.29.pdiff [5642 B]
+Get:25 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [145 kB]
+Get:24 ftp://ftp.debian.org/debian unstable/main Sources 2016-02-06-1239.29.pdiff [5642 B]
+Get:26 http://incoming.debian-ports.org/buildd unstable/main sh4 Packages [59.5 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main sh4 Packages [13.8 MB]
+Get:28 ftp://ftp.debian-ports.org/debian unreleased/main sh4 Packages [15.8 kB]
+Fetched 14.8 MB in 53s (277 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -54,15 +71,15 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 ftp://ftp.debian.org/debian unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 ftp://ftp.debian.org/debian unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 ftp://ftp.debian.org/debian unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 1s (2325 kB/s)
Download complete and in download only mode
Check architectures
@@ -74,16 +91,17 @@ 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-SwNrbQ/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-0Pebpf/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Unsupported ioctl: cmd=0x40049409
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-0Pebpf/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -100,16 +118,16 @@ 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 39 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 4 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:1 file:/«BUILDDIR»/resolver-0Pebpf/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 130 kB in 3s (34.4 kB/s)
+Fetched 130 kB in 3s (32.5 kB/s)
Selecting previously unselected package libfakeroot:sh4.
-(Reading database ...
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(Reading database ... 12094 files and directories currently installed.)
+(Reading database ...
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12907 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.
@@ -123,18 +141,19 @@ 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-LxyaHx/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-s_Z8JR/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Unsupported ioctl: cmd=0x40049409
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ Packages [744 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -148,68 +167,64 @@ Reading package lists...
Building dependency tree...
Reading state information...
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
+ autoconf autoconf-archive automake autotools-dev bash-completion
+ bsdmainutils debhelper dh-strip-nondeterminism file groff-base
+ intltool-debian libarchive-zip-perl libfile-stripnondeterminism-perl
+ libhts-dev libhts1 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libsigsegv2 libtimedate-perl libtinfo-dev m4 man-db po-debconf tabix
zlib1g-dev
Suggested packages:
- wamerican | wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
+ gnu-standards autoconf-doc libtool wamerican | wordlist whois vacation
+ dh-make 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
+ libmail-sendmail-perl
The following NEW 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
+ autoconf autoconf-archive automake autotools-dev bash-completion
+ bsdmainutils debhelper dh-strip-nondeterminism file groff-base
+ intltool-debian libarchive-zip-perl libfile-stripnondeterminism-perl
+ libhts-dev libhts1 libio-pty-perl libmagic1 libncurses5-dev libpipeline1
+ libsigsegv2 libtimedate-perl libtinfo-dev m4 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]
+0 upgraded, 28 newly installed, 0 to remove and 4 not upgraded.
+Need to get 7656 kB/7657 kB of archives.
+After this operation, 27.7 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-s_Z8JR/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [988 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:3 ftp://ftp.debian-ports.org/debian unstable/main sh4 groff-base sh4 1.22.3-7 [1288 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]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main sh4 autoconf-archive all 20150925-1 [688 kB]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main sh4 libsigsegv2 sh4 2.10-4 [29.1 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main sh4 libmagic1 sh4 1:5.25-2 [264 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main sh4 file sh4 1:5.25-2 [61.5 kB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main sh4 m4 sh4 1.4.17-5 [250 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main sh4 autoconf all 2.69-9 [338 kB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main sh4 autotools-dev all 20150820.1 [71.7 kB]
+Get:14 ftp://ftp.debian-ports.org/debian unstable/main sh4 automake all 1:1.15-3 [735 kB]
+Get:15 ftp://ftp.debian-ports.org/debian unstable/main sh4 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:16 ftp://ftp.debian-ports.org/debian unstable/main sh4 po-debconf all 1.0.19 [249 kB]
+Get:17 ftp://ftp.debian-ports.org/debian unstable/main sh4 libarchive-zip-perl all 1.56-2 [94.9 kB]
+Get:18 ftp://ftp.debian-ports.org/debian unstable/main sh4 libfile-stripnondeterminism-perl all 0.015-1 [11.0 kB]
+Get:19 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:20 ftp://ftp.debian-ports.org/debian unstable/main sh4 dh-strip-nondeterminism all 0.015-1 [6810 B]
+Get:21 ftp://ftp.debian-ports.org/debian unstable/main sh4 debhelper all 9.20160115 [827 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts1 sh4 1.3-1 [265 kB]
+Get:23 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts-dev sh4 1.3-1 [304 kB]
+Get:24 ftp://ftp.debian-ports.org/debian unstable/main sh4 libio-pty-perl sh4 1:1.08-1.1 [34.6 kB]
+Get:25 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtinfo-dev sh4 6.0+20151024-2 [73.2 kB]
+Get:26 ftp://ftp.debian-ports.org/debian unstable/main sh4 libncurses5-dev sh4 6.0+20151024-2 [165 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main sh4 tabix sh4 1.3-1 [229 kB]
+Get:28 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 18.8 MB in 49s (380 kB/s)
+Fetched 7656 kB in 56s (135 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12143 files and directories currently installed.)
+(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 ... 12956 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_1.22.3-5_sh4.deb ...
-Unpacking groff-base (1.22.3-5) ...
+Preparing to unpack .../groff-base_1.22.3-7_sh4.deb ...
+Unpacking groff-base (1.22.3-7) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.6+b1_sh4.deb ...
Unpacking bsdmainutils (9.0.6+b1) ...
@@ -219,36 +234,30 @@ Unpacking libpipeline1:sh4 (1.4.1-2) ...
Selecting previously unselected package man-db.
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 autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
+Selecting previously unselected package libsigsegv2:sh4.
+Preparing to unpack .../libsigsegv2_2.10-4_sh4.deb ...
+Unpacking libsigsegv2:sh4 (2.10-4) ...
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%3a5.25-2_sh4.deb ...
Unpacking file (1:5.25-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.6-1_sh4.deb ...
-Unpacking gettext-base (0.19.6-1) ...
-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_sh4.deb ...
-Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../archives/m4_1.4.17-5_sh4.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-9_all.deb ...
+Unpacking autoconf (2.69-9) ...
+Selecting previously unselected package autotools-dev.
+Preparing to unpack .../autotools-dev_20150820.1_all.deb ...
+Unpacking autotools-dev (20150820.1) ...
+Selecting previously unselected package automake.
+Preparing to unpack .../automake_1%3a1.15-3_all.deb ...
+Unpacking automake (1:1.15-3) ...
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) ...
@@ -259,23 +268,23 @@ 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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.015-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.015-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.015-1) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20151225_all.deb ...
-Unpacking debhelper (9.20151225) ...
+Preparing to unpack .../debhelper_9.20160115_all.deb ...
+Unpacking debhelper (9.20160115) ...
Selecting previously unselected package libhts1:sh4.
-Preparing to unpack .../libhts1_1.2.1-2_sh4.deb ...
-Unpacking libhts1:sh4 (1.2.1-2) ...
+Preparing to unpack .../archives/libhts1_1.3-1_sh4.deb ...
+Unpacking libhts1:sh4 (1.3-1) ...
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) ...
+Preparing to unpack .../libhts-dev_1.3-1_sh4.deb ...
+Unpacking libhts-dev:sh4 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1_sh4.deb ...
Unpacking libio-pty-perl (1:1.08-1.1) ...
@@ -286,50 +295,48 @@ 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_1.2.1-2_sh4.deb ...
-Unpacking tabix (1.2.1-2) ...
+Preparing to unpack .../archives/tabix_1.3-1_sh4.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-5) ...
+Setting up groff-base (1.22.3-7) ...
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: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 libunistring0:sh4 (0.9.3-5.2) ...
+Setting up autoconf-archive (20150925-1) ...
+Setting up libsigsegv2:sh4 (2.10-4) ...
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: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:sh4 (0.6.11-1) ...
-Setting up gettext (0.19.6-1) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-9) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-3) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up intltool-debian (0.35.0+20060710.4) ...
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 libfile-stripnondeterminism-perl (0.015-1) ...
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 libhts1:sh4 (1.3-1) ...
+Setting up libhts-dev:sh4 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up zlib1g-dev:sh4 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20151225) ...
+Setting up debhelper (9.20160115) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Setting up dh-strip-nondeterminism (0.015-1) ...
+Processing triggers for libc-bin (2.21-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -337,8 +344,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.1.9 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.1 bzip2_1.0.6-8+b1 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debian-ports-archive-keyring_2016.02.01 d [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -349,15 +356,14 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
@@ -377,35 +383,42 @@ SCHROOT_CHROOT_NAME=sid-sh4-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-sh4-sbuild-7486bb18-f913-4a8a-a2f9-e0ce446404e9
+SCHROOT_SESSION_ID=sid-sh4-sbuild-496666af-b742-41be-9ef6-535f3ec4abe5
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c18
+XDG_SESSION_ID=c28
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture sh4
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j1 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j1 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -427,101 +440,133 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=sh4-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/sh4-linux-gnu --libexecdir=\${prefix}/lib/sh4-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- 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/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j1 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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 -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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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
/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 -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 -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 -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 -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 -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 -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
+gcc -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
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/sh4-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
@@ -534,22 +579,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/sh4-linux-gnu/libhts.a
+ prefix=/usr
install -d debian/samtools
- 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 -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -579,6 +623,7 @@ 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
+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/
@@ -598,19 +643,20 @@ Unsupported ioctl: cmd=0x40049409
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
dh_installman -a -O--parallel
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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.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
@@ -621,8 +667,8 @@ Unsupported ioctl: cmd=0x40049409
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -650,7 +696,7 @@ Unsupported ioctl: cmd=0x40049409
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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite were not linked against libdl.so.2 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
@@ -666,14 +712,14 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/samtools/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-4_sh4.deb'.
- dpkg-genchanges -B -mdebian/sh4 buildd <buildd-vs94 at glaubitz.dialup.fu-berlin.de> >../samtools_1.2-4_sh4.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3-1_sh4.deb'.
+ dpkg-genchanges -B -mdebian/sh4 buildd <buildd-vs95 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3-1_sh4.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.2
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+ dpkg-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160114-1654
+Build finished at 20160206-1858
Finished
────────
@@ -690,60 +736,60 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_sh4.changes:
+samtools_1.3-1_sh4.changes:
───────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: sh4
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
-Maintainer: debian/sh4 buildd <buildd-vs94 at glaubitz.dialup.fu-berlin.de>
-Changed-By: Andreas Tille <tille at debian.org>
+Maintainer: debian/sh4 buildd <buildd-vs95 at glaubitz.dialup.fu-berlin.de>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- 16da434bb353ef5709e176d5e5821c12ee65281b 401466 samtools_1.2-4_sh4.deb
+ b873560655af587fb26dee0d8f15f4aac3089819 253890 samtools_1.3-1_sh4.deb
Checksums-Sha256:
- bc30b6384816635d6bc1bf17343c0d8ce993f7417ffcf221eb57b2e99714d948 401466 samtools_1.2-4_sh4.deb
+ b6a69c6fca65a4914396e79bef4e07264b5577ebe6effa85bdbd08852085bcf3 253890 samtools_1.3-1_sh4.deb
Files:
- d3cbcc9d2da78ed5b38b17e34fb339aa 401466 science optional samtools_1.2-4_sh4.deb
+ 8344f6c4519ad212d651a917ddd07105 253890 science optional samtools_1.3-1_sh4.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_sh4.deb
+samtools_1.3-1_sh4.deb
──────────────────────
new debian package, version 2.0.
- size 401466 bytes: control archive=1609 bytes.
+ size 253890 bytes: control archive=1637 bytes.
805 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 873
- Depends: libc6 (>= 2.21), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 604
+ Depends: libc6 (>= 2.21), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -756,47 +802,48 @@ samtools_1.2-4_sh4.deb
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 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 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 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 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-06 18:58 ./
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/
+drwxr-xr-x root/root 0 2016-02-06 18:58 ./usr/bin/
+-rwxr-xr-x root/root 13652 2016-02-06 18:58 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 22:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 22:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 22:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 22:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9544 2016-02-06 18:58 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9544 2016-02-06 18:58 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9564 2016-02-06 18:58 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5432 2016-02-06 18:58 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 22:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 22:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 22:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 22:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 338324 2016-02-06 18:58 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 22:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 22:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 22:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 22:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17816 2016-02-06 18:58 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 22:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 22:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 22:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 15:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 15:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 15:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 15:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 15:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 15:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-06 18:57 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-06 18:57 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-06 18:57 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-06 18:57 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-06 18:57 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -816,23 +863,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: sh4
-Build-Space: 14728
-Build-Time: 697
+Build-Space: 15376
+Build-Time: 765
Distribution: sid
Host Architecture: sh4
-Install-Time: 201
-Job: samtools_1.2-4
+Install-Time: 211
+Job: samtools_1.3-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 980
-Source-Version: 1.2-4
-Space: 14728
+Package-Time: 1071
+Source-Version: 1.3-1
+Space: 15376
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160114-1654
-Build needed 00:16:20, 14728k disc space
+Finished at 20160206-1858
+Build needed 00:17:51, 15376k disc space
Signature with key '933A5126' requested:
- signfile /var/lib/buildd/build/samtools_1.2-4_sh4.changes 933A5126
+ signfile /var/lib/buildd/build/samtools_1.3-1_sh4.changes 933A5126
Successfully signed changes file
diff --git a/x32.log b/x32.log
index 0dcc8b3..86e19a1 100644
--- a/x32.log
+++ b/x32.log
@@ -2,59 +2,49 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs76.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-4 (x32) 21 Dec 2015 15:57 ║
+║ samtools 1.3-1 (x32) 05 Feb 2016 17:45 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.2-4
-Source Version: 1.2-4
+Version: 1.3-1
+Source Version: 1.3-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: x32
Build Architecture: x32
-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.
+I: NOTICE: Log filtering will replace 'build/samtools-xeWfqH/samtools-1.3' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-xeWfqH' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-1a279431-3f8a-4b28-b779-88532cfff01f' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.debian.org/debian unstable InRelease [278 kB]
+Get:2 http://ftp.debian.org/debian unstable/main Sources.diff/Index [27.9 kB]
+Get:3 http://ftp.debian-ports.org/debian unstable InRelease [37.1 kB]
+Ign:4 http://incoming.debian-ports.org/buildd unstable InRelease
+Get:5 http://ftp.debian.org/debian unstable/main Sources 2016-02-02-1445.56.pdiff [20.6 kB]
+Get:6 http://ftp.debian.org/debian unstable/main Sources 2016-02-02-2051.26.pdiff [12.3 kB]
+Get:7 http://ftp.debian.org/debian unstable/main Sources 2016-02-03-0247.20.pdiff [7814 B]
+Get:8 http://ftp.debian.org/debian unstable/main Sources 2016-02-03-0847.44.pdiff [5373 B]
+Get:9 http://ftp.debian.org/debian unstable/main Sources 2016-02-03-1452.45.pdiff [20.5 kB]
+Get:10 http://ftp.debian.org/debian unstable/main Sources 2016-02-03-2047.23.pdiff [15.1 kB]
+Get:11 http://ftp.debian.org/debian unstable/main Sources 2016-02-04-0247.46.pdiff [26.0 kB]
+Get:12 http://ftp.debian.org/debian unstable/main Sources 2016-02-04-0851.05.pdiff [14.2 kB]
+Get:13 http://ftp.debian.org/debian unstable/main Sources 2016-02-04-1446.17.pdiff [14.1 kB]
+Get:14 http://ftp.debian.org/debian unstable/main Sources 2016-02-04-2131.08.pdiff [18.5 kB]
+Get:15 http://ftp.debian.org/debian unstable/main Sources 2016-02-05-0254.43.pdiff [5835 B]
+Get:15 http://ftp.debian.org/debian unstable/main Sources 2016-02-05-0254.43.pdiff [5835 B]
+Get:16 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [111 kB]
+Get:17 http://incoming.debian-ports.org/buildd unstable Release [43.8 kB]
+Get:18 http://ftp.debian-ports.org/debian unreleased InRelease [40.8 kB]
+Get:19 http://incoming.debian-ports.org/buildd unstable Release.gpg [836 B]
+Get:20 http://ftp.debian-ports.org/debian unstable/main x32 Packages [14.5 MB]
+Get:21 http://incoming.debian-ports.org/buildd unstable/main x32 Packages [107 kB]
+Get:22 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [183 kB]
+Fetched 15.5 MB in 12s (1211 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -67,25 +57,23 @@ 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
+https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
-git clone git://anonscm.debian.org/debian-med/samtools.git
+git clone https://anonscm.debian.org/git/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)
+Need to get 3757 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (dsc) [2150 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (tar) [3743 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3-1 (diff) [12.0 kB]
+Fetched 3757 kB in 1s (2140 kB/s)
Download complete and in download only mode
Check architectures
@@ -95,34 +83,20 @@ 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
-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.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-MmlFD4/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-MmlFD4/apt_archive ./ Packages [527 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...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -130,7 +104,6 @@ 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...
@@ -138,16 +111,16 @@ 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 0 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 11 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 file:/«BUILDDIR»/resolver-Ef3l6_/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
+Get:1 file:/«BUILDDIR»/resolver-MmlFD4/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 (110 kB/s)
+Fetched 129 kB in 1s (114 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 ... 12692 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 ... 15405 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.
@@ -156,41 +129,26 @@ 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) ...
+Processing triggers for man-db (2.7.5-1) ...
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)
-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.
+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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, 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 (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-G2K3no/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ Packages [742 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...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -198,139 +156,44 @@ 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 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
+ autoconf-archive bash-completion libhts-dev libhts1 libio-pty-perl
+ libncurses5-dev libtinfo-dev tabix
Suggested packages:
- 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
+ ncurses-doc
The following NEW 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
- 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]
+ autoconf-archive bash-completion libhts-dev libhts1 libio-pty-perl
+ libncurses5-dev libtinfo-dev sbuild-build-depends-samtools-dummy tabix
+0 upgraded, 9 newly installed, 0 to remove and 11 not upgraded.
+Need to get 1929 kB/1930 kB of archives.
+After this operation, 11.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-G2K3no/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [988 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]
+Get:3 http://ftp.debian-ports.org/debian unstable/main x32 autoconf-archive all 20150925-1 [688 kB]
+Get:4 http://ftp.debian-ports.org/debian unstable/main x32 libhts1 x32 1.3-1 [243 kB]
+Get:5 http://ftp.debian-ports.org/debian unstable/main x32 libhts-dev x32 1.3-1 [299 kB]
+Get:6 http://ftp.debian-ports.org/debian unstable/main x32 libio-pty-perl x32 1:1.08-1.1+b1 [33.8 kB]
+Get:7 http://ftp.debian-ports.org/debian unstable/main x32 libtinfo-dev x32 6.0+20151024-2 [76.5 kB]
+Get:8 http://ftp.debian-ports.org/debian unstable/main x32 libncurses5-dev x32 6.0+20151024-2 [173 kB]
+Get:9 http://ftp.debian-ports.org/debian unstable/main x32 tabix x32 1.3-1 [236 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 18.6 MB in 5s (3273 kB/s)
+Fetched 1929 kB in 3s (594 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 ... 12741 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 ... 15453 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_1.22.3-4_x32.deb ...
-Unpacking groff-base (1.22.3-4) ...
-Selecting previously unselected package bsdmainutils.
-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_2.7.5-1_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%3a5.25-2_x32.deb ...
-Unpacking libmagic1:x32 (1:5.25-2) ...
-Selecting previously unselected package file.
-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_55.1-6_x32.deb ...
-Unpacking libicu55:x32 (55.1-6) ...
-Selecting previously unselected package libxml2:x32.
-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_2.46.2-1_x32.deb ...
-Unpacking libglib2.0-0:x32 (2.46.2-1) ...
-Selecting previously unselected package libcroco3:x32.
-Preparing to unpack .../libcroco3_0.6.11-1_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) ...
-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) ...
-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_9.20151220_all.deb ...
-Unpacking debhelper (9.20151220) ...
+Selecting previously unselected package autoconf-archive.
+Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
+Unpacking autoconf-archive (20150925-1) ...
Selecting previously unselected package libhts1:x32.
-Preparing to unpack .../libhts1_1.2.1-2_x32.deb ...
-Unpacking libhts1:x32 (1.2.1-2) ...
+Preparing to unpack .../archives/libhts1_1.3-1_x32.deb ...
+Unpacking libhts1:x32 (1.3-1) ...
Selecting previously unselected package libhts-dev:x32.
-Preparing to unpack .../libhts-dev_1.2.1-2_x32.deb ...
-Unpacking libhts-dev:x32 (1.2.1-2) ...
+Preparing to unpack .../libhts-dev_1.3-1_x32.deb ...
+Unpacking libhts-dev:x32 (1.3-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_x32.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
@@ -341,61 +204,32 @@ Selecting previously unselected package libncurses5-dev:x32.
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_1.2.1-2_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+b2_x32.deb ...
-Unpacking zlib1g-dev:x32 (1:1.2.8.dfsg-2+b2) ...
+Preparing to unpack .../archives/tabix_1.3-1_x32.deb ...
+Unpacking tabix (1.3-1) ...
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) ...
+Processing triggers for man-db (2.7.5-1) ...
+Processing triggers for libc-bin (2.21-7) ...
Setting up bash-completion (1:2.1-4.2) ...
-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 (2.7.5-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up libunistring0:x32 (0.9.3-5.2) ...
-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 (55.1-6) ...
-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 (0.6.11-1) ...
-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 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 autoconf-archive (20150925-1) ...
+Setting up libhts1:x32 (1.3-1) ...
+Setting up libhts-dev:x32 (1.3-1) ...
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 tabix (1.3-1) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up dh-strip-nondeterminism (0.014-1) ...
-Processing triggers for libc-bin (2.21-4) ...
+Processing triggers for libc-bin (2.21-7) ...
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 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 [...]
+Toolchain package versions: binutils_2.26-2 dpkg-dev_1.18.4 g++-5_5.3.1-7 gcc-5_5.3.1-7 libc6-dev_2.21-7 libstdc++-5-dev_5.3.1-7 libstdc++6_5.3.1-7 linux-libc-dev_4.3.3-7
+Package versions: adduser_3.113+nmu3 apt_1.2.1 autoconf_2.69-9 autoconf-archive_20150925-1 automake_1:1.15-3 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.5 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.2 binutils_2.26-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27.1-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.25-1 cpp_4:5.3.1-1 cpp-5_5.3.1-7 dash_0.5.8-2.1 debconf_1.5.58 debconf-i18n_1.5.58 debhelper_9.20160115 debian-archive-keyring_2014.3 debianutils_4.7 dh-autore [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -405,31 +239,25 @@ Package versions: adduser_3.113+nmu3 apt_1.1.5 base-files_9.5 base-passwd_3.5.38
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 Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
+gpgv: Signature made Fri Feb 5 14:47:37 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.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_1.2-4.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: warning: failed to verify signature on ./samtools_1.3-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3
+dpkg-source: info: unpacking samtools_1.3.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3-1.debian.tar.xz
+dpkg-source: info: applying spelling.patch
+dpkg-source: info: applying literal_version.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
@@ -442,37 +270,42 @@ SCHROOT_CHROOT_NAME=sid-x32-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-x32-sbuild-0887497a-406f-4ea7-b28f-712fd7874df5
+SCHROOT_SESSION_ID=sid-x32-sbuild-1a279431-3f8a-4b28-b779-88532cfff01f
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_RUNTIME_DIR=/run/user/114
-XDG_SESSION_ID=18355
+XDG_SESSION_ID=c18679
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 1.2-4
+dpkg-buildpackage: source version 1.3-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.2
+ dpkg-source --before-build samtools-1.3
dpkg-buildpackage: host architecture x32
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
- dh_auto_clean -O--parallel
- make -j1 distclean
+ debian/rules override_dh_auto_clean
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
+touch config.mk
+dh_auto_clean --
+ make -j1 distclean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_clean -O--parallel
+ rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
@@ -494,101 +327,133 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
- dh_auto_configure -a -O--parallel
+ dh_update_autotools_config -a -O--parallel
+ debian/rules override_dh_auto_configure
+make[1]: Entering directory '/«PKGBUILDDIR»'
+touch config.mk
+aclocal --force -I /usr/share/aclocal/ -I debian/
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+autoconf
+configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
+debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
+configure.ac:40: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=x86_64-linux-gnux32 --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnux32 --libexecdir=\${prefix}/lib/x86_64-linux-gnux32 --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
+checking for gcc... gcc
+checking whether the C compiler works... yes
+checking for C compiler default output file name... a.out
+checking for suffix of executables...
+checking whether we are cross compiling... no
+checking for suffix of object files... o
+checking whether we are using the GNU C compiler... yes
+checking whether gcc accepts -g... yes
+checking for gcc option to accept ISO C89... none needed
+checking for htslib/sam.h... yes
+checking for hts_version in -lhts... yes
+checking for NcursesW wide-character library... no
+checking for Ncurses library... yes
+checking for working ncurses/curses.h... no
+checking for working ncurses.h... yes
+checking for zlib.h... yes
+checking for inflate in -lz... yes
+configure: creating ./config.status
+config.status: creating config.mk
+config.status: creating config.h
+make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_build
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnux32/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
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
+ make -j1 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
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
-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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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
-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 -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 -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 -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 -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 -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 -pthread -rdynamic -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 sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.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 bam_quickcheck.o bam_addrprg.o libb [...]
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
+gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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 -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I. -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
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 \
BGZIP=/usr/bin/bgzip
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
@@ -601,22 +466,21 @@ dh binary-arch --parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a
+ prefix=/usr
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
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
+install -p -m 644 samtools.1 misc/wgsim.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 test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
+cd test/dat && rm -f test_input_*.bam.bai
+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 xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f 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_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
@@ -638,19 +502,20 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
dh_installman -a -O--parallel
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 ./wgsim\.1 > wgsim\.1\.new
+ chmod 644 wgsim.1.new
+ mv -f wgsim.1.new wgsim.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
@@ -661,8 +526,8 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ chmod a-x usr/share/doc/samtools/NEWS.Debian 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/NEWS.Debian 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
@@ -678,59 +543,59 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/2f52985ac22ad66759f0f83fec4416994b0cd0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/2f52985ac22ad66759f0f83fec4416994b0cd0.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/2f52985ac22ad66759f0f83fec4416994b0cd0.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/a3dd0169f7ec30056c5c36d91e9b0233134794.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/a3dd0169f7ec30056c5c36d91e9b0233134794.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0f/a3dd0169f7ec30056c5c36d91e9b0233134794.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/624e41bd12e84898c21279727cbc725dd105a0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/624e41bd12e84898c21279727cbc725dd105a0.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/624e41bd12e84898c21279727cbc725dd105a0.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/c57d99e645c78814880119e811684bdfc7b71f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/c57d99e645c78814880119e811684bdfc7b71f.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5b/c57d99e645c78814880119e811684bdfc7b71f.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/92
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/92/88e583a1aace174427b1eeeaa13837d8363461.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/92/88e583a1aace174427b1eeeaa13837d8363461.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/92/88e583a1aace174427b1eeeaa13837d8363461.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6a/461ddf3a5d93f136464ae7f29a25ec75cb408a.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6a/461ddf3a5d93f136464ae7f29a25ec75cb408a.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/6a/461ddf3a5d93f136464ae7f29a25ec75cb408a.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/d0f84f7603c0c4bb671d27fe95054c3a4119c3.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/d0f84f7603c0c4bb671d27fe95054c3a4119c3.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/d0f84f7603c0c4bb671d27fe95054c3a4119c3.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
+ ln -s samtools debian/.debhelper/samtools/dbgsym-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-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)
+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/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libdl.so.2 (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 [...]
+ install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-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=0fa3dd0169f7ec30056c5c36d91e9b0233134794 142f52985ac22ad66759f0f83fec4416994b0cd0 5bc57d99e645c78814880119e811684b [...]
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
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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}
@@ -740,28 +605,27 @@ 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
+ (cd debian/.debhelper/samtools/dbgsym-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/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-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 -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_x32.deb'.
dpkg-deb --build debian/samtools ..
-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-deb: building package 'samtools' in '../samtools_1.3-1_x32.deb'.
+ dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.3-1_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-source --after-build samtools-1.3
+dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20151221-1559
+Build finished at 20160205-1746
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 │
@@ -773,108 +637,108 @@ W: line 8 [experimental-x32-sbuild] source-root-users: Configuration key name
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.2-4_x32.changes:
+samtools_1.3-1_x32.changes:
───────────────────────────
Format: 1.8
-Date: Mon, 21 Dec 2015 13:49:05 +0100
+Date: Fri, 05 Feb 2016 08:32:40 +0000
Source: samtools
Binary: samtools samtools-test
Architecture: x32
-Version: 1.2-4
+Version: 1.3-1
Distribution: sid
Urgency: medium
Maintainer: Debian/x32 buildd <buildd at vs76.physik.fu-berlin.de>
-Changed-By: Andreas Tille <tille at debian.org>
+Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
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
+ samtools (1.3-1) unstable; urgency=medium
+ .
+ [ Charles Plessy ]
+ 95c561d Merge tag '1.3' into debian/unstable
.
+ [ Sascha Steinbiss ]
* Team upload
- * Fix synopsis
- * Fix Vcs-Browser
- * Add lintian-override to document that the language extensions are used
- internally
+ * Adapt to new build system
+ * Use secure Vcs-Git
+ * Patch autoconf not to use make to extract version
+ * Clean up d/copyright
* Fix spelling
- * Fix Mayhem issues caused by unlimited reads of gz input
- Closes: #716199, #716197
- * Provide some more manpages
Checksums-Sha1:
- 6008a94a46547075945de1803f65a49eb0abc070 400108 samtools-dbgsym_1.2-4_x32.deb
- 84fe7a2cb520a82fe58c55080030b3b1a189f096 394188 samtools_1.2-4_x32.deb
+ 155fd711ba7c3310bc52dde7aabcb5796a545707 445664 samtools-dbgsym_1.3-1_x32.deb
+ a8a6f4efae51c45b0c68d5a882ffc1f30c8de551 247346 samtools_1.3-1_x32.deb
Checksums-Sha256:
- 3b3f8c650c590a483e36149ac79a201dd2d1e4cafd96a2bc9f60a2adc06998c6 400108 samtools-dbgsym_1.2-4_x32.deb
- 53cd76579dbf55718aa41dd1feea82b9f5fb22ad991830a40e0cdce342af8ba1 394188 samtools_1.2-4_x32.deb
+ 4a6c4e83618d4f1c22319d98e54223ef92039a0706b93a9d2a5b852f70836f99 445664 samtools-dbgsym_1.3-1_x32.deb
+ 4611b15f5647ff1519c8b5b2cb91b64361d2a6351e622bbdd9ec0baeacec472d 247346 samtools_1.3-1_x32.deb
Files:
- 23f3b6f007f9461e5ea34917bdef64c1 400108 debug extra samtools-dbgsym_1.2-4_x32.deb
- b5bbf799311fccfbc4d00fa1460690e3 394188 science optional samtools_1.2-4_x32.deb
+ bd478b2aa7b7c973f60b990d5ee9cedc 445664 debug extra samtools-dbgsym_1.3-1_x32.deb
+ dbd556e7f7a5f5d000d8a2c47801dc05 247346 science optional samtools_1.3-1_x32.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.2-4_x32.deb
+samtools-dbgsym_1.3-1_x32.deb
─────────────────────────────
new debian package, version 2.0.
- size 400108 bytes: control archive=812 bytes.
+ size 445664 bytes: control archive=816 bytes.
644 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: x32
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 466
- Depends: samtools (= 1.2-4)
+ Installed-Size: 499
+ Depends: samtools (= 1.3-1)
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
+ Build-Ids: 0fa3dd0169f7ec30056c5c36d91e9b0233134794 142f52985ac22ad66759f0f83fec4416994b0cd0 5bc57d99e645c78814880119e811684bdfc7b71f 6a461ddf3a5d93f136464ae7f29a25ec75cb408a 8d624e41bd12e84898c21279727cbc725dd105a0 91d0f84f7603c0c4bb671d27fe95054c3a4119c3 9288e583a1aace174427b1eeeaa13837d8363461
+
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/0f/
+-rw-r--r-- root/root 17668 2016-02-05 17:46 ./usr/lib/debug/.build-id/0f/a3dd0169f7ec30056c5c36d91e9b0233134794.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/14/
+-rw-r--r-- root/root 419648 2016-02-05 17:46 ./usr/lib/debug/.build-id/14/2f52985ac22ad66759f0f83fec4416994b0cd0.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/5b/
+-rw-r--r-- root/root 9764 2016-02-05 17:46 ./usr/lib/debug/.build-id/5b/c57d99e645c78814880119e811684bdfc7b71f.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/6a/
+-rw-r--r-- root/root 7192 2016-02-05 17:46 ./usr/lib/debug/.build-id/6a/461ddf3a5d93f136464ae7f29a25ec75cb408a.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/8d/
+-rw-r--r-- root/root 9752 2016-02-05 17:46 ./usr/lib/debug/.build-id/8d/624e41bd12e84898c21279727cbc725dd105a0.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/91/
+-rw-r--r-- root/root 17184 2016-02-05 17:46 ./usr/lib/debug/.build-id/91/d0f84f7603c0c4bb671d27fe95054c3a4119c3.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/lib/debug/.build-id/92/
+-rw-r--r-- root/root 9800 2016-02-05 17:46 ./usr/lib/debug/.build-id/92/88e583a1aace174427b1eeeaa13837d8363461.debug
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-02-05 17:46 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3-1_x32.deb
──────────────────────
new debian package, version 2.0.
- size 394188 bytes: control archive=1607 bytes.
- 806 bytes, 17 lines control
- 1828 bytes, 31 lines md5sums
+ size 247346 bytes: control archive=1633 bytes.
+ 805 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.2-4
+ Version: 1.3-1
Architecture: x32
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1042
- Depends: libc6 (>= 2.16), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 681
+ Depends: libc6 (>= 2.16), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -887,47 +751,48 @@ samtools_1.2-4_x32.deb
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 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 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 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 2015-12-21 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 2015-12-21 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
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/bin/
+-rwxr-xr-x root/root 18056 2016-02-05 17:46 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-12-15 22:26 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-12-15 22:26 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-12-15 22:26 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-12-15 22:26 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9832 2016-02-05 17:46 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9832 2016-02-05 17:46 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9872 2016-02-05 17:46 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5704 2016-02-05 17:46 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-12-15 22:26 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2015-12-15 22:26 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-12-15 22:26 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-12-15 22:26 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 413288 2016-02-05 17:46 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-12-15 22:26 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-12-15 22:26 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-12-15 22:26 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-12-15 22:26 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 18144 2016-02-05 17:46 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2015-12-15 22:26 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-12-15 22:26 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-12-15 22:26 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-02-05 15:41 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 1031 2016-02-05 15:41 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3925 2016-02-05 15:41 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2711 2016-02-05 15:41 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-02-05 15:41 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-02-05 15:41 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-02-05 17:46 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 18900 2016-02-05 17:46 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-02-05 17:46 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-02-05 17:46 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -940,34 +805,30 @@ drwxr-xr-x root/root 0 2015-12-21 15:59 ./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: 15852
-Build-Time: 41
+Build-Space: 16392
+Build-Time: 40
Distribution: sid
Host Architecture: x32
-Install-Time: 22
-Job: samtools_1.2-4
+Install-Time: 11
+Job: samtools_1.3-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 99
-Source-Version: 1.2-4
-Space: 15852
+Package-Time: 70
+Source-Version: 1.3-1
+Space: 16392
Status: successful
-Version: 1.2-4
+Version: 1.3-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20151221-1559
-Build needed 00:01:39, 15852k disc space
+Finished at 20160205-1746
+Build needed 00:01:10, 16392k disc space
Signature with key 'A644D214' requested:
- signfile /var/lib/buildd/build/samtools_1.2-4_x32.changes A644D214
+ signfile /var/lib/buildd/build/samtools_1.3-1_x32.changes A644D214
Successfully signed changes file
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git
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