[med-svn] samtools 04/04: Build logs for version 1.3.1-1.
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 2c825b152c5bc378d9520e61a8d697b732bf3475
Author: Charles Plessy <plessy at debian.org>
Date: Wed Apr 27 09:54:57 2016 +0900
Build logs for version 1.3.1-1.
---
all.log | 2355 ++++++++++++++++++++++++++++++++++++++++++++++++
arm64.log => amd64.log | 1576 +++++++++++++++++---------------
arm64.log | 1481 ++++++++++++++++--------------
armel.log | 1571 +++++++++++++++++++++-----------
i386.log | 1470 ++++++++++++++++--------------
kfreebsd-amd64.log | 1408 ++++++++++++++++-------------
kfreebsd-i386.log | 1408 ++++++++++++++++-------------
m68k.log | 926 ++++++++++---------
mips64el.log | 1453 +++++++++++++++--------------
mipsel.log | 1557 +++++++++++++++++++++-----------
ppc64el.log | 1475 ++++++++++++++++--------------
sh4.log | 740 ++++++++-------
x32.log | 2134 +++++++++++++++++++++++++++++++++++--------
13 files changed, 12717 insertions(+), 6837 deletions(-)
diff --git a/all.log b/all.log
new file mode 100644
index 0000000..02d9255
--- /dev/null
+++ b/all.log
@@ -0,0 +1,2355 @@
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-bm-01.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.3.1-1 (amd64) 26 Apr 2016 12:30 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.3.1-1
+Source Version: 1.3.1-1
+Distribution: sid
+Machine Architecture: amd64
+Host Architecture: amd64
+Build Architecture: amd64
+
+I: NOTICE: Log filtering will replace 'build/samtools-jJZtkF/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-jJZtkF' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-92deb64f-c678-4452-b6f8-129e1b87328b' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://mirror.bm.debian.org/debian unstable InRelease [196 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:4 http://mirror.bm.debian.org/debian unstable/main Sources [6767 kB]
+Get:5 http://mirror.bm.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:6 http://mirror.bm.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:7 http://mirror.bm.debian.org/debian unstable/main amd64 Packages [7074 kB]
+Get:8 http://mirror.bm.debian.org/debian unstable/contrib amd64 Packages [53.9 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [144 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib amd64 Packages [2612 B]
+Get:14 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main amd64 Packages [7074 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib amd64 Packages [53.9 kB]
+Fetched 28.8 MB in 6s (4648 kB/s)
+Reading package lists...
+W: No sandbox user '_apt' on the system, can not drop privileges
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+W: apt-cache output for different version
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+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 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (57.9 MB/s)
+Download complete and in download only mode
+
+Check architectures
+───────────────────
+
+sh: 1: gcc: not found
+sbuild: warning: couldn't determine gcc system type, falling back to default (native compilation)
+
+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-WJY4Qe/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-WJY4Qe/apt_archive ./ Packages [525 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 NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+0 upgraded, 1 newly installed, 0 to remove and 31 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-WJY4Qe/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 ... 12358 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 (>= 4:5.3), 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-TE8fJl/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ Packages [747 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 autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf tabix zlib1g-dev
+Suggested packages:
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
+Recommended packages:
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 31 not upgraded.
+Need to get 25.8 MB/25.8 MB of archives.
+After this operation, 89.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-TE8fJl/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [992 B]
+Get:2 http://mirror.bm.debian.org/debian unstable/main amd64 bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://mirror.bm.debian.org/debian unstable/main amd64 groff-base amd64 1.22.3-7 [1175 kB]
+Get:4 http://mirror.bm.debian.org/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB]
+Get:5 http://mirror.bm.debian.org/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 kB]
+Get:6 http://mirror.bm.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB]
+Get:7 http://mirror.bm.debian.org/debian unstable/main amd64 man-db amd64 2.7.5-1 [1003 kB]
+Get:8 http://mirror.bm.debian.org/debian unstable/main amd64 autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://mirror.bm.debian.org/debian unstable/main amd64 libunistring0 amd64 0.9.3-5.2+b1 [288 kB]
+Get:10 http://mirror.bm.debian.org/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2g-2 [1286 kB]
+Get:11 http://mirror.bm.debian.org/debian unstable/main amd64 libmagic1 amd64 1:5.25-2 [255 kB]
+Get:12 http://mirror.bm.debian.org/debian unstable/main amd64 file amd64 1:5.25-2 [61.5 kB]
+Get:13 http://mirror.bm.debian.org/debian unstable/main amd64 gettext-base amd64 0.19.7-2 [115 kB]
+Get:14 http://mirror.bm.debian.org/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB]
+Get:15 http://mirror.bm.debian.org/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB]
+Get:16 http://mirror.bm.debian.org/debian unstable/main amd64 libidn11 amd64 1.32-3 [113 kB]
+Get:17 http://mirror.bm.debian.org/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB]
+Get:18 http://mirror.bm.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-3 [111 kB]
+Get:19 http://mirror.bm.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.8-1 [49.5 kB]
+Get:20 http://mirror.bm.debian.org/debian unstable/main amd64 libgnutls30 amd64 3.4.11-3 [791 kB]
+Get:21 http://mirror.bm.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-8 [12.2 kB]
+Get:22 http://mirror.bm.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5 [60.2 kB]
+Get:23 http://mirror.bm.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5 [114 kB]
+Get:24 http://mirror.bm.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5 [309 kB]
+Get:25 http://mirror.bm.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5 [152 kB]
+Get:26 http://mirror.bm.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB]
+Get:27 http://mirror.bm.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB]
+Get:28 http://mirror.bm.debian.org/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB]
+Get:29 http://mirror.bm.debian.org/debian unstable/main amd64 libicu55 amd64 55.1-7 [7649 kB]
+Get:30 http://mirror.bm.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.3+dfsg1-1 [916 kB]
+Get:31 http://mirror.bm.debian.org/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB]
+Get:32 http://mirror.bm.debian.org/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB]
+Get:33 http://mirror.bm.debian.org/debian unstable/main amd64 autoconf all 2.69-10 [338 kB]
+Get:34 http://mirror.bm.debian.org/debian unstable/main amd64 autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://mirror.bm.debian.org/debian unstable/main amd64 automake all 1:1.15-4 [735 kB]
+Get:36 http://mirror.bm.debian.org/debian unstable/main amd64 autopoint all 0.19.7-2 [424 kB]
+Get:37 http://mirror.bm.debian.org/debian unstable/main amd64 libglib2.0-0 amd64 2.48.0-1 [2700 kB]
+Get:38 http://mirror.bm.debian.org/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB]
+Get:39 http://mirror.bm.debian.org/debian unstable/main amd64 gettext amd64 0.19.7-2 [1482 kB]
+Get:40 http://mirror.bm.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://mirror.bm.debian.org/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB]
+Get:42 http://mirror.bm.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://mirror.bm.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://mirror.bm.debian.org/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://mirror.bm.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://mirror.bm.debian.org/debian unstable/main amd64 libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://mirror.bm.debian.org/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB]
+Get:48 http://mirror.bm.debian.org/debian unstable/main amd64 debhelper all 9.20160403 [800 kB]
+Get:49 http://mirror.bm.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.9.2-1 [76.1 kB]
+Get:50 http://mirror.bm.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1+b1 [60.0 kB]
+Get:51 http://mirror.bm.debian.org/debian unstable/main amd64 libssh2-1 amd64 1.5.0-2.1 [133 kB]
+Get:52 http://mirror.bm.debian.org/debian unstable/main amd64 libcurl3-gnutls amd64 7.47.0-1 [273 kB]
+Get:53 http://mirror.bm.debian.org/debian unstable/main amd64 libhts1 amd64 1.3.1-1 [257 kB]
+Get:54 http://mirror.bm.debian.org/debian unstable/main amd64 libhts-dev amd64 1.3.1-1 [315 kB]
+Get:55 http://mirror.bm.debian.org/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b1 [33.1 kB]
+Get:56 http://mirror.bm.debian.org/debian unstable/main amd64 libtinfo-dev amd64 6.0+20160319-1 [77.6 kB]
+Get:57 http://mirror.bm.debian.org/debian unstable/main amd64 libncurses5-dev amd64 6.0+20160319-1 [174 kB]
+Get:58 http://mirror.bm.debian.org/debian unstable/main amd64 tabix amd64 1.3.1-1 [252 kB]
+Get:59 http://mirror.bm.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 25.8 MB in 0s (42.1 MB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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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 ... 12358 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-7_amd64.deb ...
+Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:amd64.
+Preparing to unpack .../libbsd0_0.8.3-1_amd64.deb ...
+Unpacking libbsd0:amd64 (0.8.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.10_amd64.deb ...
+Unpacking bsdmainutils (9.0.10) ...
+Selecting previously unselected package libpipeline1:amd64.
+Preparing to unpack .../libpipeline1_1.4.1-2_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.1-2) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.5-1_amd64.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 libunistring0:amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package libssl1.0.2:amd64.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_amd64.deb ...
+Unpacking libssl1.0.2:amd64 (1.0.2g-2) ...
+Selecting previously unselected package libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.25-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.25-2) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-2_amd64.deb ...
+Unpacking file (1:5.25-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.7-2_amd64.deb ...
+Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:amd64.
+Preparing to unpack .../libnettle6_3.2-1_amd64.deb ...
+Unpacking libnettle6:amd64 (3.2-1) ...
+Selecting previously unselected package libhogweed4:amd64.
+Preparing to unpack .../libhogweed4_3.2-1_amd64.deb ...
+Unpacking libhogweed4:amd64 (3.2-1) ...
+Selecting previously unselected package libidn11:amd64.
+Preparing to unpack .../libidn11_1.32-3_amd64.deb ...
+Unpacking libidn11:amd64 (1.32-3) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.2.1-4_amd64.deb ...
+Unpacking libffi6:amd64 (3.2.1-4) ...
+Selecting previously unselected package libp11-kit0:amd64.
+Preparing to unpack .../libp11-kit0_0.23.2-3_amd64.deb ...
+Unpacking libp11-kit0:amd64 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:amd64.
+Preparing to unpack .../libtasn1-6_4.8-1_amd64.deb ...
+Unpacking libtasn1-6:amd64 (4.8-1) ...
+Selecting previously unselected package libgnutls30:amd64.
+Preparing to unpack .../libgnutls30_3.4.11-3_amd64.deb ...
+Unpacking libgnutls30:amd64 (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:amd64.
+Preparing to unpack .../libkeyutils1_1.5.9-8_amd64.deb ...
+Unpacking libkeyutils1:amd64 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:amd64.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libkrb5support0:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:amd64.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libk5crypto3:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:amd64.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libkrb5-3:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:amd64.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:amd64.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_amd64.deb ...
+Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:amd64.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_amd64.deb ...
+Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:amd64.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_amd64.deb ...
+Unpacking libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ...
+Selecting previously unselected package libicu55:amd64.
+Preparing to unpack .../libicu55_55.1-7_amd64.deb ...
+Unpacking libicu55:amd64 (55.1-7) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libsigsegv2:amd64.
+Preparing to unpack .../libsigsegv2_2.10-5_amd64.deb ...
+Unpacking libsigsegv2:amd64 (2.10-5) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../archives/m4_1.4.17-5_amd64.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
+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%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Preparing to unpack .../libglib2.0-0_2.48.0-1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.48.0-1) ...
+Selecting previously unselected package libcroco3:amd64.
+Preparing to unpack .../libcroco3_0.6.11-1_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.11-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.7-2_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_1.0.19_all.deb ...
+Unpacking po-debconf (1.0.19) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
+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_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:amd64.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_amd64.deb ...
+Unpacking libnghttp2-14:amd64 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:amd64.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_amd64.deb ...
+Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:amd64.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_amd64.deb ...
+Unpacking libssh2-1:amd64 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:amd64.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_amd64.deb ...
+Unpacking libcurl3-gnutls:amd64 (7.47.0-1) ...
+Selecting previously unselected package libhts1:amd64.
+Preparing to unpack .../libhts1_1.3.1-1_amd64.deb ...
+Unpacking libhts1:amd64 (1.3.1-1) ...
+Selecting previously unselected package libhts-dev:amd64.
+Preparing to unpack .../libhts-dev_1.3.1-1_amd64.deb ...
+Unpacking libhts-dev:amd64 (1.3.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
+Selecting previously unselected package libtinfo-dev:amd64.
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_amd64.deb ...
+Unpacking libtinfo-dev:amd64 (6.0+20160319-1) ...
+Selecting previously unselected package libncurses5-dev:amd64.
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (6.0+20160319-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.3.1-1_amd64.deb ...
+Unpacking tabix (1.3.1-1) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
+Setting up groff-base (1.22.3-7) ...
+Setting up libbsd0:amd64 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
+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: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 autoconf-archive (20150925-1) ...
+Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
+Setting up libssl1.0.2:amd64 (1.0.2g-2) ...
+Setting up libmagic1:amd64 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
+Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:amd64 (3.2-1) ...
+Setting up libhogweed4:amd64 (3.2-1) ...
+Setting up libidn11:amd64 (1.32-3) ...
+Setting up libffi6:amd64 (3.2.1-4) ...
+Setting up libp11-kit0:amd64 (0.23.2-3) ...
+Setting up libtasn1-6:amd64 (4.8-1) ...
+Setting up libgnutls30:amd64 (3.4.11-3) ...
+Setting up libkeyutils1:amd64 (1.5.9-8) ...
+Setting up libkrb5support0:amd64 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:amd64 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:amd64 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ...
+Setting up libicu55:amd64 (55.1-7) ...
+Setting up libxml2:amd64 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:amd64 (2.10-5) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-10) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-4) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:amd64 (2.48.0-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:amd64 (0.6.11-1) ...
+Setting up gettext (0.19.7-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:amd64 (1.9.2-1) ...
+Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:amd64 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:amd64 (7.47.0-1) ...
+Setting up libhts1:amd64 (1.3.1-1) ...
+Setting up libhts-dev:amd64 (1.3.1-1) ...
+Setting up libio-pty-perl (1:1.08-1.1+b1) ...
+Setting up libtinfo-dev:amd64 (6.0+20160319-1) ...
+Setting up libncurses5-dev:amd64 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.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=parallel=4
+HOME=/sbuild-nonexistent
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+SCHROOT_ALIAS_NAME=sid-amd64-sbuild
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-amd64-sbuild-92deb64f-c678-4452-b6f8-129e1b87328b
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_RUNTIME_DIR=/run/user/2952
+XDG_SESSION_ID=11156
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.3.1-1
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/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-indep
+dh build-indep --parallel
+ dh_testdir -i -O--parallel
+ dh_update_autotools_config -i -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:42: 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:42: the top level
+autoconf
+configure.ac:42: 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:42: the top level
+dh_auto_configure -- --with-htslib=system
+ ./configure --build=x86_64-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/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
+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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -j4 test VERBOSE=1 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/vCZxCGf7MG/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/vCZxCGf7MG/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/vCZxCGf7MG/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/vCZxCGf7MG/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/vCZxCGf7MG/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/vCZxCGf7MG/large_chrom.bam
+
+ ERR:
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/vCZxCGf7MG/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/vCZxCGf7MG/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/vCZxCGf7MG/mpileup.bam.list -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/vCZxCGf7MG/mpileup.cram.list -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/vCZxCGf7MG/mpileup.bam.list -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/vCZxCGf7MG/mpileup.cram.list -f /tmp/vCZxCGf7MG/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/vCZxCGf7MG/mpileup.cram.list -f /tmp/vCZxCGf7MG/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/vCZxCGf7MG/mpileup.cram.list -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vCZxCGf7MG/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/vCZxCGf7MG/mpileup.ref.fa.gz -r17:1050-1060 /tmp/vCZxCGf7MG/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ 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
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+.. ok
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare .. ok
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare .. ok
+
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
+
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 8: BAM -> CRAM with UR -> SAM .. ok
+
+ 9: SAM -> BAM (M5 header tags) .. ok
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 11: CRAM -> BAM with UR .. ok
+
+ 12: CRAM -> BAM with M5 .. ok
+
+ 13: SAM -> SAM via stdout .. ok
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout .. ok
+
+ 16: SAM from stdin -> SAM .. ok
+
+ 17: BAM from stdin -> SAM .. ok
+
+ 18: CRAM from stdin -> SAM .. ok
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input) .. ok
+
+ 23: No headers (BAM input) .. ok
+
+ 24: No headers (CRAM input) .. ok
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input) .. ok
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input) .. ok
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input) .. ok
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input) .. ok
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input) .. ok
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input) .. ok
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input) .. ok
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input) .. ok
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/vCZxCGf7MG/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/vCZxCGf7MG/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/vCZxCGf7MG/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/vCZxCGf7MG/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/vCZxCGf7MG/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/vCZxCGf7MG/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/vCZxCGf7MG/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/vCZxCGf7MG/view.001.fogn (CRAM input).. ok
+
+ 67: Filter -l Library 2 (SAM input) .. ok
+
+ 68: Count -l Library 2 (SAM input) .. ok
+
+ 69: Filter -l Library 2 (BAM input) .. ok
+
+ 70: Count -l Library 2 (BAM input) .. ok
+
+ 71: Filter -l Library 2 (CRAM input) .. ok
+
+ 72: Count -l Library 2 (CRAM input) .. ok
+
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
+
+ 78: Count -l Library 3 (CRAM input) .. ok
+
+ 79: Filter -q 50 (SAM input) .. ok
+
+ 80: Count -q 50 (SAM input) .. ok
+
+ 81: Filter -q 50 (BAM input) .. ok
+
+ 82: Count -q 50 (BAM input) .. ok
+
+ 83: Filter -q 50 (CRAM input) .. ok
+
+ 84: Count -q 50 (CRAM input) .. ok
+
+ 85: Filter -q 99 (SAM input) .. ok
+
+ 86: Count -q 99 (SAM input) .. ok
+
+ 87: Filter -q 99 (BAM input) .. ok
+
+ 88: Count -q 99 (BAM input) .. ok
+
+ 89: Filter -q 99 (CRAM input) .. ok
+
+ 90: Count -q 99 (CRAM input) .. ok
+
+ 91: Filter -q 100 (SAM input) .. ok
+
+ 92: Count -q 100 (SAM input) .. ok
+
+ 93: Filter -q 100 (BAM input) .. ok
+
+ 94: Count -q 100 (BAM input) .. ok
+
+ 95: Filter -q 100 (CRAM input) .. ok
+
+ 96: Count -q 100 (CRAM input) .. ok
+
+ 97: Filter -x fa (SAM input) .. ok
+
+ 98: Count -x fa (SAM input) .. ok
+
+ 99: Filter -x fa (BAM input) .. ok
+
+ 100: Count -x fa (BAM input) .. ok
+
+ 101: Filter -x fa (CRAM input) .. ok
+
+ 102: Count -x fa (CRAM input) .. ok
+
+ 103: Filter -x fa -x ha (SAM input) .. ok
+
+ 104: Count -x fa -x ha (SAM input) .. ok
+
+ 105: Filter -x fa -x ha (BAM input) .. ok
+
+ 106: Count -x fa -x ha (BAM input) .. ok
+
+ 107: Filter -x fa -x ha (CRAM input) .. ok
+
+ 108: Count -x fa -x ha (CRAM input) .. ok
+
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 110: Count -x fa -r grp2 (SAM input) .. ok
+
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 112: Count -x fa -r grp2 (BAM input) .. ok
+
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 116: Count -x RG -r grp2 (SAM input) .. ok
+
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 118: Count -x RG -r grp2 (BAM input) .. ok
+
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 121: Filter -m 10 (SAM input) .. ok
+
+ 122: Count -m 10 (SAM input) .. ok
+
+ 123: Filter -m 10 (BAM input) .. ok
+
+ 124: Count -m 10 (BAM input) .. ok
+
+ 125: Filter -m 10 (CRAM input) .. ok
+
+ 126: Count -m 10 (CRAM input) .. ok
+
+ 127: Filter -m 11 (SAM input) .. ok
+
+ 128: Count -m 11 (SAM input) .. ok
+
+ 129: Filter -m 11 (BAM input) .. ok
+
+ 130: Count -m 11 (BAM input) .. ok
+
+ 131: Filter -m 11 (CRAM input) .. ok
+
+ 132: Count -m 11 (CRAM input) .. ok
+
+ 133: Filter -m 15 (SAM input) .. ok
+
+ 134: Count -m 15 (SAM input) .. ok
+
+ 135: Filter -m 15 (BAM input) .. ok
+
+ 136: Count -m 15 (BAM input) .. ok
+
+ 137: Filter -m 15 (CRAM input) .. ok
+
+ 138: Count -m 15 (CRAM input) .. ok
+
+ 139: Filter -m 16 (SAM input) .. ok
+
+ 140: Count -m 16 (SAM input) .. ok
+
+ 141: Filter -m 16 (BAM input) .. ok
+
+ 142: Count -m 16 (BAM input) .. ok
+
+ 143: Filter -m 16 (CRAM input) .. ok
+
+ 144: Count -m 16 (CRAM input) .. ok
+
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 146: Region Z (BAM input) .. ok
+
+ 147: Count Z (BAM input) .. ok
+
+ 148: Region Z (CRAM input) .. ok
+
+ 149: Count Z (CRAM input) .. ok
+
+ 150: Region Z:30 (BAM input) .. ok
+
+ 151: Count Z:30 (BAM input) .. ok
+
+ 152: Region Z:30 (CRAM input) .. ok
+
+ 153: Count Z:30 (CRAM input) .. ok
+
+ 154: Region Z:20-40 (BAM input) .. ok
+
+ 155: Count Z:20-40 (BAM input) .. ok
+
+ 156: Region Z:20-40 (CRAM input) .. ok
+
+ 157: Count Z:20-40 (CRAM input) .. ok
+
+ 158: Region ref1 (BAM input) .. ok
+
+ 159: Count ref1 (BAM input) .. ok
+
+ 160: Region ref1 (CRAM input) .. ok
+
+ 161: Count ref1 (CRAM input) .. ok
+
+ 162: Region ref1:15 (BAM input) .. ok
+
+ 163: Count ref1:15 (BAM input) .. ok
+
+ 164: Region ref1:15 (CRAM input) .. ok
+
+ 165: Count ref1:15 (CRAM input) .. ok
+
+ 166: Region ref1:15-45 (BAM input) .. ok
+
+ 167: Count ref1:15-45 (BAM input) .. ok
+
+ 168: Region ref1:15-45 (CRAM input) .. ok
+
+ 169: Count ref1:15-45 (CRAM input) .. ok
+
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 186: Region -f 128 ref1 (BAM input) .. ok
+
+ 187: Count -f 128 ref1 (BAM input) .. ok
+
+ 188: Region -f 128 ref1 (CRAM input) .. ok
+
+ 189: Count -f 128 ref1 (CRAM input) .. ok
+
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 254: Make BAM with no M5/UR tags .. ok
+
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 267: Make CRAM with no UR field .. ok
+
+ 268: Decoding CRAM with no UR field via -T .. ok
+
+ 269: CIGAR B-operator removal .. ok
+
+ 270: Big SAM -> BAM .. ok
+
+ 271: Big SAM -> BAM (2 threads) .. ok
+
+ 272: Big SAM -> BAM (4 threads) .. ok
+
+ 273: Big SAM -> CRAM .. ok
+
+ 274: Big SAM -> CRAM (2 threads) .. ok
+
+ 275: Big SAM -> CRAM (4 threads) .. ok
+
+ 276: Subsample 0.2 (SAM input) ............ ok
+
+ 277: Subsample 0.5 (SAM input) ............ ok
+
+ 278: Subsample 0.8 (SAM input) ............ ok
+
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
+
+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 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
+
+ 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 .. ok
+
+ 1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+ 2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+ 3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+ 4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+ 5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+ 6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
+.. ok
+
+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
+
+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
+
+test_depad:
+ Generate BAM file .. ok
+
+ depad (SAM input) .. ok
+
+ depad -s (SAM input) .. ok
+
+ depad -u (SAM input) .. ok
+
+ depad -1 (SAM input) .. ok
+
+ depad (BAM input) .. ok
+
+ depad -s (BAM input) .. ok
+
+ depad -u (BAM input) .. ok
+
+ 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
+
+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
+
+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/5_insert_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+4
+.. ok
+
+test_stats:
+ /«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/8_secondary.sam | tail -n+4
+.. ok
+
+test_stats:
+ /«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 -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/OYC65QNb08 - /«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/vCZxCGf7MG/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/vCZxCGf7MG/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/vCZxCGf7MG/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:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
+
+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 .. 423
+ passed .. 403
+ failed .. 0
+ expected failure .. 20
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
+
+Expected passes: 124
+Unexpected passes: 0
+Expected failures: 0
+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
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-indep
+dh binary-indep --parallel
+ dh_testroot -i -O--parallel
+ dh_prep -i -O--parallel
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr
+ install -d debian/samtools-test
+ 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 -i -O--parallel
+ install -d debian/samtools-test/usr/share/samtools
+ cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/
+ dh_installdocs -i -O--parallel
+ install -d debian/samtools-test/usr/share/doc/samtools-test
+ install -p -m0644 debian/copyright debian/samtools-test/usr/share/doc/samtools-test/copyright
+ dh_installchangelogs -i -O--parallel
+ install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
+ install -p -m0644 debian/NEWS debian/samtools-test/usr/share/doc/samtools-test/NEWS.Debian
+ dh_perl -i -O--parallel
+ (grep -a -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl) > debian/samtools-test.substvars.new
+ mv debian/samtools-test.substvars.new debian/samtools-test.substvars
+ dh_link -i -O--parallel
+ dh_strip_nondeterminism -i -O--parallel
+ dh_compress -i -O--parallel
+ cd debian/samtools-test
+ chmod a-x usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog.Debian
+ gzip -9nf usr/share/doc/samtools-test/NEWS.Debian usr/share/doc/samtools-test/changelog.Debian
+ cd '/«PKGBUILDDIR»'
+ dh_fixperms -i -O--parallel
+ find debian/samtools-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
+ find debian/samtools-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
+ find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools-test/usr/lib/x86_64-linux-gnu/perl5/5.22 debian/samtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools-test -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-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
+ dh_installdeb -i -O--parallel
+ install -d debian/samtools-test/DEBIAN
+ dh_gencontrol -i -O--parallel
+ echo misc:Depends= >> debian/samtools-test.substvars
+ echo misc:Pre-Depends= >> debian/samtools-test.substvars
+ dpkg-gencontrol -psamtools-test -ldebian/changelog -Tdebian/samtools-test.substvars -Pdebian/samtools-test
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools-test: unused substitution variable ${perl:Depends}
+ chmod 0644 debian/samtools-test/DEBIAN/control
+ chown 0:0 debian/samtools-test/DEBIAN/control
+ dh_md5sums -i -O--parallel
+ (cd debian/samtools-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/samtools-test/DEBIAN/md5sums
+ chown 0:0 debian/samtools-test/DEBIAN/md5sums
+ dh_builddeb -i -O--parallel
+ dpkg-deb --build debian/samtools-test ..
+dpkg-deb: building package 'samtools-test' in '../samtools-test_1.3.1-1_all.deb'.
+ dpkg-genchanges -A -mall Build Daemon (x86-bm-01) <buildd_all-x86-bm-01 at buildd.debian.org> >../samtools_1.3.1-1_all.changes
+dpkg-genchanges: binary-only arch-indep upload (source code and arch-specific packages not included)
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-buildpackage: binary-only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20160426-1232
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.3.1-1_all.changes:
+─────────────────────────────
+
+Format: 1.8
+Date: Tue, 26 Apr 2016 21:12:05 +0900
+Source: samtools
+Binary: samtools samtools-test
+Architecture: all
+Version: 1.3.1-1
+Distribution: sid
+Urgency: medium
+Maintainer: all Build Daemon (x86-bm-01) <buildd_all-x86-bm-01 at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Changes:
+ samtools (1.3.1-1) unstable; urgency=medium
+ .
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
+Checksums-Sha1:
+ 17ea94dce52c268a3b5179e287b1892e98905650 1938970 samtools-test_1.3.1-1_all.deb
+Checksums-Sha256:
+ bcd0baf50b806f41707192be61f94fbf496aff5b0ef973daeadbabd2e31b9185 1938970 samtools-test_1.3.1-1_all.deb
+Files:
+ 9982e23b083f4462db2cabd3bba1f842 1938970 science optional samtools-test_1.3.1-1_all.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-test_1.3.1-1_all.deb
+─────────────────────────────
+
+ new debian package, version 2.0.
+ size 1938970 bytes: control archive=7061 bytes.
+ 495 bytes, 15 lines control
+ 23828 bytes, 288 lines md5sums
+ Package: samtools-test
+ Source: samtools
+ Version: 1.3.1-1
+ Architecture: all
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 9516
+ Recommends: libio-pty-perl
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: test files for the samtools package
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format.
+ .
+ This package contains test files for the samtools package.
+
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/doc/samtools-test/
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools-test/NEWS.Debian.gz
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools-test/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools-test/copyright
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/
+-rw-r--r-- root/root 1712 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/1_fixup.sam
+-rw-r--r-- root/root 1928 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/1_fixup.sam.expected.err
+-rw-r--r-- root/root 1712 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam
+-rw-r--r-- root/root 1928 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/2_fixup_orphan.sam.expected.err
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected
+-rw-r--r-- root/root 79 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/3_fixup.sam.expected.err
+-rw-r--r-- root/root 1690 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam
+-rw-r--r-- root/root 1923 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/addrprg/4_fixup_norg.sam.expected.err
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/1.1.fq.expected
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/1.2.fq.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/1.stdout.expected
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/2.1.fq.expected
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/2.2.fq.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/2.s.fq.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/2.stdout.expected
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/3.1.fq.expected
+-rw-r--r-- root/root 767 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/3.2.fq.expected
+-rw-r--r-- root/root 41 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/3.s.fq.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/3.stdout.expected
+-rw-r--r-- root/root 712 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/4.1.fq.expected
+-rw-r--r-- root/root 712 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/4.2.fq.expected
+-rw-r--r-- root/root 96 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/4.s.fq.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/bam2fq/4.stdout.expected
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/dat/
+-rw-r--r-- root/root 5471 2016-04-22 09:22 ./usr/share/samtools/test/dat/bam2fq.001.sam
+-rw-r--r-- root/root 5573 2016-04-22 09:22 ./usr/share/samtools/test/dat/bam2fq.002.sam
+-rw-r--r-- root/root 5493 2016-04-22 09:22 ./usr/share/samtools/test/dat/bam2fq.003.sam
+-rw-r--r-- root/root 1292 2016-04-22 09:22 ./usr/share/samtools/test/dat/cat.hdr
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/dat/cram_md5/
+-rw-r--r-- root/root 57 2016-04-22 09:22 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
+-rw-r--r-- root/root 61 2016-04-22 09:22 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
+-rw-r--r-- root/root 36 2016-04-22 09:22 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
+-rw-r--r-- root/root 31 2016-04-22 09:22 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
+-rw-r--r-- root/root 42 2016-04-22 09:22 ./usr/share/samtools/test/dat/depad.001.fa
+-rw-r--r-- root/root 16 2016-04-22 09:22 ./usr/share/samtools/test/dat/depad.001.fa.fai
+-rw-r--r-- root/root 7964 2016-04-22 09:22 ./usr/share/samtools/test/dat/depad.001p.sam
+-rw-r--r-- root/root 7970 2016-04-22 09:22 ./usr/share/samtools/test/dat/depad.001u.sam
+-rw-r--r-- root/root 1511 2016-04-22 09:22 ./usr/share/samtools/test/dat/dict.fa
+-rw-r--r-- root/root 1109 2016-04-22 09:22 ./usr/share/samtools/test/dat/dict.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/dat/empty.expected
+-rw-r--r-- root/root 624 2016-04-22 09:22 ./usr/share/samtools/test/dat/large_chrom.out
+-rw-r--r-- root/root 5090 2016-04-22 09:22 ./usr/share/samtools/test/dat/large_chrom.sam
+-rw-r--r-- root/root 92 2016-04-22 09:22 ./usr/share/samtools/test/dat/large_chrom_bai_index.err
+-rw-r--r-- root/root 350835 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.1.sam
+-rw-r--r-- root/root 104818 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.2.sam
+-rw-r--r-- root/root 105780 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.3.sam
+-rw-r--r-- root/root 78 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.err.1
+-rw-r--r-- root/root 2716 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.out.1
+-rw-r--r-- root/root 81480 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.out.2
+-rw-r--r-- root/root 295 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.out.3
+-rw-r--r-- root/root 113718 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.out.4
+-rw-r--r-- root/root 4284 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.ref.fa
+-rw-r--r-- root/root 17 2016-04-22 09:22 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai
+-rw-r--r-- root/root 759 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_a.bam
+-rw-r--r-- root/root 264 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai.expected
+-rw-r--r-- root/root 1429 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_a.sam
+-rw-r--r-- root/root 1576 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_a_regex.sam
+-rw-r--r-- root/root 686 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_b.bam
+-rw-r--r-- root/root 1252 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_b.sam
+-rw-r--r-- root/root 1369 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_b_regex.sam
+-rw-r--r-- root/root 692 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_c.bam
+-rw-r--r-- root/root 1293 2016-04-22 09:22 ./usr/share/samtools/test/dat/test_input_1_c.sam
+-rw-r--r-- root/root 1335 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.001.01.bed
+-rw-r--r-- root/root 1134 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.001.02.bed
+-rw-r--r-- root/root 130 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.001.fa
+-rw-r--r-- root/root 33 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.001.fa.fai
+-rw-r--r-- root/root 5060 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.001.sam
+-rw-r--r-- root/root 1313 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.002.01.bed
+-rw-r--r-- root/root 1302 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.002.02.bed
+-rw-r--r-- root/root 64 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.002.fa
+-rw-r--r-- root/root 13 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.002.fa.fai
+-rw-r--r-- root/root 3692 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.002.sam
+-rw-r--r-- root/root 2142 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.003.expected.sam
+-rw-r--r-- root/root 2224 2016-04-22 09:22 ./usr/share/samtools/test/dat/view.003.sam
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/
+-rw-r--r-- root/root 894 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/1_coord_sort.sam
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected
+-rw-r--r-- root/root 82 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err
+-rw-r--r-- root/root 1047 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam
+-rw-r--r-- root/root 1102 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected
+-rw-r--r-- root/root 715 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam
+-rw-r--r-- root/root 715 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected
+-rw-r--r-- root/root 715 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam
+-rw-r--r-- root/root 715 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected
+-rw-r--r-- root/root 715 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/5_ct.sam
+-rw-r--r-- root/root 735 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/5_ct.sam.expected
+-rw-r--r-- root/root 735 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/6_ct_replace.sam
+-rw-r--r-- root/root 735 2016-04-22 09:22 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/idxstats/
+-rw-r--r-- root/root 58 2016-04-22 09:22 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/merge/
+-rw-r--r-- root/root 1228 2016-04-22 09:22 ./usr/share/samtools/test/merge/2.merge.expected.bam
+-rw-r--r-- root/root 1233 2016-04-22 09:22 ./usr/share/samtools/test/merge/3.merge.expected.bam
+-rw-r--r-- root/root 174 2016-04-22 09:22 ./usr/share/samtools/test/merge/3.merge.expected.err
+-rw-r--r-- root/root 689 2016-04-22 09:22 ./usr/share/samtools/test/merge/4.merge.expected.bam
+-rw-r--r-- root/root 1115 2016-04-22 09:22 ./usr/share/samtools/test/merge/5.merge.expected.bam
+-rw-r--r-- root/root 4353 2016-04-22 09:22 ./usr/share/samtools/test/merge/5.merge.expected.sam
+-rw-r--r-- root/root 899 2016-04-22 09:22 ./usr/share/samtools/test/merge/6.merge.expected.bam
+-rw-r--r-- root/root 1056 2016-04-22 09:22 ./usr/share/samtools/test/merge/7.merge.expected.bam
+-rw-r--r-- root/root 46 2016-04-22 09:22 ./usr/share/samtools/test/merge/test_3.fofn
+-rw-r--r-- root/root 15918 2016-04-22 09:22 ./usr/share/samtools/test/merge/test_bam_translate.c
+-rw-r--r-- root/root 184 2016-04-22 09:22 ./usr/share/samtools/test/merge/test_header.sam
+-rw-r--r-- root/root 3552 2016-04-22 09:22 ./usr/share/samtools/test/merge/test_rtrans_build.c
+-rw-r--r-- root/root 17450 2016-04-22 09:22 ./usr/share/samtools/test/merge/test_trans_tbl_init.c
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/mpileup/
+-rw-r--r-- root/root 525 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/1read.bam
+-rw-r--r-- root/root 5 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/1read.sam
+-rw-r--r-- root/root 1886 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/anomalous.sam
+-rw-r--r-- root/root 293 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#ID.bam
+-rw-r--r-- root/root 377 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#ID2.bam
+-rw-r--r-- root/root 265 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#clip.bam
+-rw-r--r-- root/root 299 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#pad1.bam
+-rw-r--r-- root/root 349 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#pad2.bam
+-rw-r--r-- root/root 382 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1#pad3.bam
+-rw-r--r-- root/root 29 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1.fa
+-rw-r--r-- root/root 26 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/c1.fa.fai
+-rw-r--r-- root/root 557 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#5b.bam
+-rw-r--r-- root/root 416 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#5b.bam.bai
+-rw-r--r-- root/root 13183 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#5b.cram
+-rw-r--r-- root/root 75 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#5b.cram.crai
+-rw-r--r-- root/root 2033 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#5b.sam
+-rw-r--r-- root/root 345315 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#large_seq.bam
+-rw-r--r-- root/root 233 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#unmap.bam
+-rw-r--r-- root/root 896 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#unmap1.bam
+-rw-r--r-- root/root 1344 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce#unmap2.bam
+-rw-r--r-- root/root 1060702 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce.fa
+-rw-r--r-- root/root 230 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/ce.fa.fai
+-rw-r--r-- root/root 252022 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/deep.sam
+-rw-r--r-- root/root 1658 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/depth.reg
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/mpileup/expected/
+-rw-r--r-- root/root 596103 2016-04-26 12:32 ./usr/share/samtools/test/mpileup/expected/1.out.f3-6.gz
+-rw-r--r-- root/root 607 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/10.out
+-rw-r--r-- root/root 238 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/11.out
+-rw-r--r-- root/root 306 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/12.out
+-rw-r--r-- root/root 163523 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/13.out
+-rw-r--r-- root/root 282158 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/14.out
+-rw-r--r-- root/root 282158 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/15.out
+-rw-r--r-- root/root 162702 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/16.out
+-rw-r--r-- root/root 163523 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/17.out
+-rw-r--r-- root/root 163523 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/18.out
+-rw-r--r-- root/root 162702 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/19.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/2.out
+-rw-r--r-- root/root 58055 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/20.out
+-rw-r--r-- root/root 162702 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/21.out
+-rw-r--r-- root/root 162702 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/22.out
+-rw-r--r-- root/root 2252 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/23.out
+-rw-r--r-- root/root 2352 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/24.out
+-rw-r--r-- root/root 2352 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/25.out
+-rw-r--r-- root/root 1706 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/26.out
+-rw-r--r-- root/root 2112 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/27.out
+-rw-r--r-- root/root 165459 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/28.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/29.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/3.out
+-rw-r--r-- root/root 1501 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/30.out
+-rw-r--r-- root/root 1503 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/31.out
+-rw-r--r-- root/root 1501 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/32.out
+-rw-r--r-- root/root 176 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/33.out
+-rw-r--r-- root/root 166 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/34.out
+-rw-r--r-- root/root 59199 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/35.out
+-rw-r--r-- root/root 163523 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/37.out
+-rw-r--r-- root/root 2882 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/38.out
+-rw-r--r-- root/root 475 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/39.out
+-rw-r--r-- root/root 4352 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/4.out
+-rw-r--r-- root/root 2155 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/40.out
+-rw-r--r-- root/root 559 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/41.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/42.out
+-rw-r--r-- root/root 103144 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/43.out
+-rw-r--r-- root/root 103144 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/44.out
+-rw-r--r-- root/root 111941 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/45.out
+-rw-r--r-- root/root 111941 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/46.out
+-rw-r--r-- root/root 5 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/47.out
+-rw-r--r-- root/root 383633 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/48.out
+-rw-r--r-- root/root 383633 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/49.out
+-rw-r--r-- root/root 244 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/5.out
+-rw-r--r-- root/root 427813 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/50.out
+-rw-r--r-- root/root 404148 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/51.out
+-rw-r--r-- root/root 482633 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/52.out
+-rw-r--r-- root/root 138 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/53.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/54.out
+-rw-r--r-- root/root 139 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/55.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/56.out
+-rw-r--r-- root/root 139 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/57.out
+-rw-r--r-- root/root 138 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/58.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/59.out
+-rw-r--r-- root/root 362 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/6.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/60.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/61.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/62.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/63.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/64.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/65.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/66.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/67.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/68.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/69.out
+-rw-r--r-- root/root 458 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/7.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/70.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/71.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/72.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/73.out
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/74.out
+-rw-r--r-- root/root 140 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/75.out
+-rw-r--r-- root/root 221725 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/76.out
+-rw-r--r-- root/root 318473 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/77.out
+-rw-r--r-- root/root 204 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/8.out
+-rw-r--r-- root/root 137 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/9.out
+-rw-r--r-- root/root 45 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d1_1.out
+-rw-r--r-- root/root 86 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d1_12.out
+-rw-r--r-- root/root 45 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d1_2.out
+-rw-r--r-- root/root 48 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d2_12r.out
+-rw-r--r-- root/root 191 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d3_12.out
+-rw-r--r-- root/root 115 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d3_12r1a.out
+-rw-r--r-- root/root 58 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d3_12r2a.out
+-rw-r--r-- root/root 573 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d4_12.out
+-rw-r--r-- root/root 165 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d4_12b.out
+-rw-r--r-- root/root 115 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/expected/d4_12r.out
+-rw-r--r-- root/root 1561 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/indels.sam
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/
+-rw-r--r-- root/root 200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
+-rw-r--r-- root/root 200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
+-rw-r--r-- root/root 4200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
+-rw-r--r-- root/root 200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
+-rw-r--r-- root/root 200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
+-rw-r--r-- root/root 200 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
+-rw-r--r-- root/root 280 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup-E.bam
+-rw-r--r-- root/root 71637 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.1.bam
+-rw-r--r-- root/root 776 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.1.bam.bai
+-rw-r--r-- root/root 31556 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.2.bam
+-rw-r--r-- root/root 31216 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.3.bam
+-rw-r--r-- root/root 4284 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.ref.fa
+-rw-r--r-- root/root 17 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.ref.fa.fai
+-rw-r--r-- root/root 7811 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/mpileup.reg
+-rw-r--r-- root/root 793 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/overlap50.sam
+-rw-r--r-- root/root 583 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/overlapIllumina.bam
+-rw-r--r-- root/root 250 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/regions
+-rwxr-xr-x root/root 4770 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/regression.sh
+-rw-r--r-- root/root 279 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx#depth1.sam
+-rw-r--r-- root/root 279 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx#depth2.sam
+-rw-r--r-- root/root 215 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx#minimal.bam
+-rw-r--r-- root/root 247 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx#triplet.bam
+-rw-r--r-- root/root 17 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx.bed
+-rw-r--r-- root/root 8 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx.bed2
+-rw-r--r-- root/root 56 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx.fa
+-rw-r--r-- root/root 29 2016-04-22 09:22 ./usr/share/samtools/test/mpileup/xx.fa.fai
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/quickcheck/
+-rw-r--r-- root/root 1228 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/1.quickcheck.badeof.bam
+-rw-r--r-- root/root 1233 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/2.quickcheck.badheader.bam
+-rw-r--r-- root/root 1228 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/3.quickcheck.ok.bam
+-rw-r--r-- root/root 1233 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/4.quickcheck.ok.bam
+-rw-r--r-- root/root 11960 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/5.quickcheck.truncated.cram
+-rw-r--r-- root/root 79 2016-04-22 09:22 ./usr/share/samtools/test/quickcheck/all.expected
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/reheader/
+-rw-r--r-- root/root 5079 2016-04-22 09:22 ./usr/share/samtools/test/reheader/1_view1.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/reheader/1_view1.sam.expected.err
+-rw-r--r-- root/root 5079 2016-04-22 09:22 ./usr/share/samtools/test/reheader/2_view1.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/reheader/2_view1.sam.expected.err
+-rw-r--r-- root/root 5079 2016-04-22 09:22 ./usr/share/samtools/test/reheader/3_view1.sam.expected
+-rw-r--r-- root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/reheader/3_view1.sam.expected.err
+-rw-r--r-- root/root 1477 2016-04-22 09:22 ./usr/share/samtools/test/reheader/hdr.sam
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/split/
+-rw-r--r-- root/root 3612 2016-04-22 09:22 ./usr/share/samtools/test/split/test_count_rg.c
+-rw-r--r-- root/root 3974 2016-04-22 09:22 ./usr/share/samtools/test/split/test_expand_format_string.c
+-rw-r--r-- root/root 5216 2016-04-22 09:22 ./usr/share/samtools/test/split/test_filter_header_rg.c
+-rw-r--r-- root/root 6823 2016-04-22 09:22 ./usr/share/samtools/test/split/test_parse_args.c
+drwxr-xr-x root/root 0 2016-04-26 12:32 ./usr/share/samtools/test/stat/
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/1.stats.expected
+-rw-r--r-- root/root 61938 2016-04-22 09:22 ./usr/share/samtools/test/stat/10.stats.expected
+-rw-r--r-- root/root 433 2016-04-22 09:22 ./usr/share/samtools/test/stat/10_map_cigar.sam
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_a_1.expected.bamstat
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/10_map_cigar.sam_s1_b_1.expected.bamstat
+-rw-r--r-- root/root 232 2016-04-22 09:22 ./usr/share/samtools/test/stat/1_map_cigar.sam
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/1_map_cigar.sam_s1_a_1.expected.bamstat
+-rw-r--r-- root/root 61934 2016-04-22 09:22 ./usr/share/samtools/test/stat/2.stats.expected
+-rw-r--r-- root/root 232 2016-04-22 09:22 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam
+-rw-r--r-- root/root 60553 2016-04-22 09:22 ./usr/share/samtools/test/stat/3.stats.expected
+-rw-r--r-- root/root 232 2016-04-22 09:22 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/4.stats.expected
+-rw-r--r-- root/root 234 2016-04-22 09:22 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam
+-rw-r--r-- root/root 61957 2016-04-22 09:22 ./usr/share/samtools/test/stat/5.stats.expected
+-rw-r--r-- root/root 236 2016-04-22 09:22 ./usr/share/samtools/test/stat/5_insert_cigar.sam
+-rw-r--r-- root/root 61957 2016-04-22 09:22 ./usr/share/samtools/test/stat/6.stats.expected
+-rw-r--r-- root/root 61971 2016-04-22 09:22 ./usr/share/samtools/test/stat/7.stats.expected
+-rw-r--r-- root/root 301 2016-04-22 09:22 ./usr/share/samtools/test/stat/7_supp.sam
+-rw-r--r-- root/root 61957 2016-04-22 09:22 ./usr/share/samtools/test/stat/8.stats.expected
+-rw-r--r-- root/root 328 2016-04-22 09:22 ./usr/share/samtools/test/stat/8_secondary.sam
+-rw-r--r-- root/root 61935 2016-04-22 09:22 ./usr/share/samtools/test/stat/9.stats.expected
+-rw-r--r-- root/root 109 2016-04-22 09:22 ./usr/share/samtools/test/stat/test.fa
+-rw-r--r-- root/root 18 2016-04-22 09:22 ./usr/share/samtools/test/stat/test.fa.fai
+-rw-r--r-- root/root 2011 2016-04-22 09:22 ./usr/share/samtools/test/test.c
+-rw-r--r-- root/root 1361 2016-04-22 09:22 ./usr/share/samtools/test/test.h
+-rwxr-xr-x root/root 96931 2016-04-22 09:22 ./usr/share/samtools/test/test.pl
+drwxr-xr-x root/root 0 2016-04-22 09:22 ./usr/share/samtools/test/tview/
+-rw-r--r-- root/root 2445 2016-04-22 09:22 ./usr/share/samtools/test/tview/test_get_rg_sample.c
+-rw-r--r-- root/root 3476 2016-04-22 09:22 ./usr/share/samtools/test/vcf-miniview.c
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: amd64
+Build-Space: 26976
+Build-Time: 119
+Distribution: sid
+Host Architecture: amd64
+Install-Time: 16
+Job: samtools_1.3.1-1
+Machine Architecture: amd64
+Package: samtools
+Package-Time: 154
+Source-Version: 1.3.1-1
+Space: 26976
+Status: successful
+Version: 1.3.1-1
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20160426-1232
+Build needed 00:02:34, 26976k disc space
+Signature with key 'A835E6E2' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_all.changes A835E6E2
+
+Successfully signed changes file
diff --git a/arm64.log b/amd64.log
similarity index 51%
copy from arm64.log
copy to amd64.log
index 0d79756..f1f5dc0 100644
--- a/arm64.log
+++ b/amd64.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-linaro-03.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on babin.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (arm64) 05 Feb 2016 16:17 ║
+║ samtools 1.3.1-1 (amd64) 26 Apr 2016 12:29 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
-Machine Architecture: armhf
-Host Architecture: arm64
-Build Architecture: arm64
+Machine Architecture: amd64
+Host Architecture: amd64
+Build Architecture: amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-NbrYv3/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-NbrYv3' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-1f3b6367-0ff9-4b46-bd25-d245123de362' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://mirror.1und1.de/debian unstable InRelease [196 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://mirror.1und1.de/debian unstable/main Sources [6767 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:6 http://mirror.1und1.de/debian unstable/contrib Sources [48.6 kB]
+Get:7 http://mirror.1und1.de/debian unstable/non-free Sources [84.1 kB]
+Get:8 http://mirror.1und1.de/debian unstable/main amd64 Packages [7074 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [144 kB]
+Get:13 http://mirror.1und1.de/debian unstable/contrib amd64 Packages [53.9 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib amd64 Packages [2612 B]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main amd64 Packages [7074 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib amd64 Packages [53.9 kB]
+Fetched 28.8 MB in 7s (3901 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 14s (261 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 3s (1030 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,15 @@ 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-SmTVOu/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-EeHKd3/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-EeHKd3/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 +104,28 @@ 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 10 not upgraded.
-Need to get 0 B/770 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 31 not upgraded.
+Need to get 0 B/774 B of archives.
After this operation, 0 B of additional disk space will be used.
-Get:1 file:/«BUILDDIR»/resolver-SmTVOu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-EeHKd3/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 25%
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(Reading database ... 40%
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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.)
+(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 ... 12358 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 (>= 4:5.3), 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-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]
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-kNRu64/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ Packages [743 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,132 +139,216 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 31 not upgraded.
+Need to get 25.8 MB/25.8 MB of archives.
+After this operation, 89.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-kNRu64/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 http://mirror.1und1.de/debian unstable/main amd64 bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://mirror.1und1.de/debian unstable/main amd64 groff-base amd64 1.22.3-7 [1175 kB]
+Get:4 http://mirror.1und1.de/debian unstable/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB]
+Get:5 http://mirror.1und1.de/debian unstable/main amd64 bsdmainutils amd64 9.0.10 [184 kB]
+Get:6 http://mirror.1und1.de/debian unstable/main amd64 libpipeline1 amd64 1.4.1-2 [27.6 kB]
+Get:7 http://mirror.1und1.de/debian unstable/main amd64 man-db amd64 2.7.5-1 [1003 kB]
+Get:8 http://mirror.1und1.de/debian unstable/main amd64 autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://mirror.1und1.de/debian unstable/main amd64 libunistring0 amd64 0.9.3-5.2+b1 [288 kB]
+Get:10 http://mirror.1und1.de/debian unstable/main amd64 libssl1.0.2 amd64 1.0.2g-2 [1286 kB]
+Get:11 http://mirror.1und1.de/debian unstable/main amd64 libmagic1 amd64 1:5.25-2 [255 kB]
+Get:12 http://mirror.1und1.de/debian unstable/main amd64 file amd64 1:5.25-2 [61.5 kB]
+Get:13 http://mirror.1und1.de/debian unstable/main amd64 gettext-base amd64 0.19.7-2 [115 kB]
+Get:14 http://mirror.1und1.de/debian unstable/main amd64 libnettle6 amd64 3.2-1 [191 kB]
+Get:15 http://mirror.1und1.de/debian unstable/main amd64 libhogweed4 amd64 3.2-1 [136 kB]
+Get:16 http://mirror.1und1.de/debian unstable/main amd64 libidn11 amd64 1.32-3 [113 kB]
+Get:17 http://mirror.1und1.de/debian unstable/main amd64 libffi6 amd64 3.2.1-4 [20.4 kB]
+Get:18 http://mirror.1und1.de/debian unstable/main amd64 libp11-kit0 amd64 0.23.2-3 [111 kB]
+Get:19 http://mirror.1und1.de/debian unstable/main amd64 libtasn1-6 amd64 4.8-1 [49.5 kB]
+Get:20 http://mirror.1und1.de/debian unstable/main amd64 libgnutls30 amd64 3.4.11-3 [791 kB]
+Get:21 http://mirror.1und1.de/debian unstable/main amd64 libkeyutils1 amd64 1.5.9-8 [12.2 kB]
+Get:22 http://mirror.1und1.de/debian unstable/main amd64 libkrb5support0 amd64 1.13.2+dfsg-5 [60.2 kB]
+Get:23 http://mirror.1und1.de/debian unstable/main amd64 libk5crypto3 amd64 1.13.2+dfsg-5 [114 kB]
+Get:24 http://mirror.1und1.de/debian unstable/main amd64 libkrb5-3 amd64 1.13.2+dfsg-5 [309 kB]
+Get:25 http://mirror.1und1.de/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.13.2+dfsg-5 [152 kB]
+Get:26 http://mirror.1und1.de/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.26.dfsg1-15 [66.9 kB]
+Get:27 http://mirror.1und1.de/debian unstable/main amd64 libsasl2-2 amd64 2.1.26.dfsg1-15 [103 kB]
+Get:28 http://mirror.1und1.de/debian unstable/main amd64 libldap-2.4-2 amd64 2.4.42+dfsg-2+b2 [222 kB]
+Get:29 http://mirror.1und1.de/debian unstable/main amd64 libicu55 amd64 55.1-7 [7649 kB]
+Get:30 http://mirror.1und1.de/debian unstable/main amd64 libxml2 amd64 2.9.3+dfsg1-1 [916 kB]
+Get:31 http://mirror.1und1.de/debian unstable/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB]
+Get:32 http://mirror.1und1.de/debian unstable/main amd64 m4 amd64 1.4.17-5 [255 kB]
+Get:33 http://mirror.1und1.de/debian unstable/main amd64 autoconf all 2.69-10 [338 kB]
+Get:34 http://mirror.1und1.de/debian unstable/main amd64 autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://mirror.1und1.de/debian unstable/main amd64 automake all 1:1.15-4 [735 kB]
+Get:36 http://mirror.1und1.de/debian unstable/main amd64 autopoint all 0.19.7-2 [424 kB]
+Get:37 http://mirror.1und1.de/debian unstable/main amd64 libglib2.0-0 amd64 2.48.0-1 [2700 kB]
+Get:38 http://mirror.1und1.de/debian unstable/main amd64 libcroco3 amd64 0.6.11-1 [143 kB]
+Get:39 http://mirror.1und1.de/debian unstable/main amd64 gettext amd64 0.19.7-2 [1482 kB]
+Get:40 http://mirror.1und1.de/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://mirror.1und1.de/debian unstable/main amd64 po-debconf all 1.0.19 [249 kB]
+Get:42 http://mirror.1und1.de/debian unstable/main amd64 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://mirror.1und1.de/debian unstable/main amd64 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://mirror.1und1.de/debian unstable/main amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://mirror.1und1.de/debian unstable/main amd64 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://mirror.1und1.de/debian unstable/main amd64 libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://mirror.1und1.de/debian unstable/main amd64 dh-autoreconf all 12 [15.8 kB]
+Get:48 http://mirror.1und1.de/debian unstable/main amd64 debhelper all 9.20160403 [800 kB]
+Get:49 http://mirror.1und1.de/debian unstable/main amd64 libnghttp2-14 amd64 1.9.2-1 [76.1 kB]
+Get:50 http://mirror.1und1.de/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d-1+b1 [60.0 kB]
+Get:51 http://mirror.1und1.de/debian unstable/main amd64 libssh2-1 amd64 1.5.0-2.1 [133 kB]
+Get:52 http://mirror.1und1.de/debian unstable/main amd64 libcurl3-gnutls amd64 7.47.0-1 [273 kB]
+Get:53 http://mirror.1und1.de/debian unstable/main amd64 libhts1 amd64 1.3.1-1 [257 kB]
+Get:54 http://mirror.1und1.de/debian unstable/main amd64 libhts-dev amd64 1.3.1-1 [315 kB]
+Get:55 http://mirror.1und1.de/debian unstable/main amd64 libio-pty-perl amd64 1:1.08-1.1+b1 [33.1 kB]
+Get:56 http://mirror.1und1.de/debian unstable/main amd64 libtinfo-dev amd64 6.0+20160319-1 [77.6 kB]
+Get:57 http://mirror.1und1.de/debian unstable/main amd64 libncurses5-dev amd64 6.0+20160319-1 [174 kB]
+Get:58 http://mirror.1und1.de/debian unstable/main amd64 tabix amd64 1.3.1-1 [252 kB]
+Get:59 http://mirror.1und1.de/debian unstable/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-2+b1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 20.0 MB in 6s (3012 kB/s)
+Fetched 25.8 MB in 2s (11.5 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12358 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.3-7_arm64.deb ...
+Preparing to unpack .../groff-base_1.22.3-7_amd64.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:amd64.
+Preparing to unpack .../libbsd0_0.8.3-1_amd64.deb ...
+Unpacking libbsd0:amd64 (0.8.3-1) ...
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_1.4.1-2_arm64.deb ...
-Unpacking libpipeline1:arm64 (1.4.1-2) ...
+Preparing to unpack .../bsdmainutils_9.0.10_amd64.deb ...
+Unpacking bsdmainutils (9.0.10) ...
+Selecting previously unselected package libpipeline1:amd64.
+Preparing to unpack .../libpipeline1_1.4.1-2_amd64.deb ...
+Unpacking libpipeline1:amd64 (1.4.1-2) ...
Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.5-1_arm64.deb ...
+Preparing to unpack .../man-db_2.7.5-1_amd64.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) ...
-Selecting previously unselected package libmagic1:arm64.
-Preparing to unpack .../libmagic1_1%3a5.25-2_arm64.deb ...
-Unpacking libmagic1:arm64 (1:5.25-2) ...
+Selecting previously unselected package libunistring0:amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
+Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package libssl1.0.2:amd64.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_amd64.deb ...
+Unpacking libssl1.0.2:amd64 (1.0.2g-2) ...
+Selecting previously unselected package libmagic1:amd64.
+Preparing to unpack .../libmagic1_1%3a5.25-2_amd64.deb ...
+Unpacking libmagic1:amd64 (1:5.25-2) ...
Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.25-2_arm64.deb ...
+Preparing to unpack .../file_1%3a5.25-2_amd64.deb ...
Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.7-2_arm64.deb ...
+Preparing to unpack .../gettext-base_0.19.7-2_amd64.deb ...
Unpacking gettext-base (0.19.7-2) ...
-Selecting previously unselected package libicu55:arm64.
-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 libnettle6:amd64.
+Preparing to unpack .../libnettle6_3.2-1_amd64.deb ...
+Unpacking libnettle6:amd64 (3.2-1) ...
+Selecting previously unselected package libhogweed4:amd64.
+Preparing to unpack .../libhogweed4_3.2-1_amd64.deb ...
+Unpacking libhogweed4:amd64 (3.2-1) ...
+Selecting previously unselected package libidn11:amd64.
+Preparing to unpack .../libidn11_1.32-3_amd64.deb ...
+Unpacking libidn11:amd64 (1.32-3) ...
+Selecting previously unselected package libffi6:amd64.
+Preparing to unpack .../libffi6_3.2.1-4_amd64.deb ...
+Unpacking libffi6:amd64 (3.2.1-4) ...
+Selecting previously unselected package libp11-kit0:amd64.
+Preparing to unpack .../libp11-kit0_0.23.2-3_amd64.deb ...
+Unpacking libp11-kit0:amd64 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:amd64.
+Preparing to unpack .../libtasn1-6_4.8-1_amd64.deb ...
+Unpacking libtasn1-6:amd64 (4.8-1) ...
+Selecting previously unselected package libgnutls30:amd64.
+Preparing to unpack .../libgnutls30_3.4.11-3_amd64.deb ...
+Unpacking libgnutls30:amd64 (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:amd64.
+Preparing to unpack .../libkeyutils1_1.5.9-8_amd64.deb ...
+Unpacking libkeyutils1:amd64 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:amd64.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libkrb5support0:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:amd64.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libk5crypto3:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:amd64.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libkrb5-3:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:amd64.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_amd64.deb ...
+Unpacking libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:amd64.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_amd64.deb ...
+Unpacking libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:amd64.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_amd64.deb ...
+Unpacking libsasl2-2:amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:amd64.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_amd64.deb ...
+Unpacking libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ...
+Selecting previously unselected package libicu55:amd64.
+Preparing to unpack .../libicu55_55.1-7_amd64.deb ...
+Unpacking libicu55:amd64 (55.1-7) ...
+Selecting previously unselected package libxml2:amd64.
+Preparing to unpack .../libxml2_2.9.3+dfsg1-1_amd64.deb ...
+Unpacking libxml2:amd64 (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libsigsegv2:amd64.
+Preparing to unpack .../libsigsegv2_2.10-5_amd64.deb ...
+Unpacking libsigsegv2:amd64 (2.10-5) ...
Selecting previously unselected package m4.
-Preparing to unpack .../archives/m4_1.4.17-5_arm64.deb ...
+Preparing to unpack .../archives/m4_1.4.17-5_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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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_2.46.2-3_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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
+Selecting previously unselected package libglib2.0-0:amd64.
+Preparing to unpack .../libglib2.0-0_2.48.0-1_amd64.deb ...
+Unpacking libglib2.0-0:amd64 (2.48.0-1) ...
+Selecting previously unselected package libcroco3:amd64.
+Preparing to unpack .../libcroco3_0.6.11-1_amd64.deb ...
+Unpacking libcroco3:amd64 (0.6.11-1) ...
Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.7-2_arm64.deb ...
+Preparing to unpack .../gettext_0.19.7-2_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 ...
@@ -276,96 +357,137 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
-Selecting previously unselected package libhts1:arm64.
-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_1.3-1_arm64.deb ...
-Unpacking libhts-dev:arm64 (1.3-1) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:amd64.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_amd64.deb ...
+Unpacking libnghttp2-14:amd64 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:amd64.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_amd64.deb ...
+Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:amd64.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_amd64.deb ...
+Unpacking libssh2-1:amd64 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:amd64.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_amd64.deb ...
+Unpacking libcurl3-gnutls:amd64 (7.47.0-1) ...
+Selecting previously unselected package libhts1:amd64.
+Preparing to unpack .../libhts1_1.3.1-1_amd64.deb ...
+Unpacking libhts1:amd64 (1.3.1-1) ...
+Selecting previously unselected package libhts-dev:amd64.
+Preparing to unpack .../libhts-dev_1.3.1-1_amd64.deb ...
+Unpacking libhts-dev:amd64 (1.3.1-1) ...
Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_arm64.deb ...
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_amd64.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
-Selecting previously unselected package libtinfo-dev:arm64.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_arm64.deb ...
-Unpacking libtinfo-dev:arm64 (6.0+20151024-2) ...
-Selecting previously unselected package libncurses5-dev:arm64.
-Preparing to unpack .../libncurses5-dev_6.0+20151024-2_arm64.deb ...
-Unpacking libncurses5-dev:arm64 (6.0+20151024-2) ...
+Selecting previously unselected package libtinfo-dev:amd64.
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_amd64.deb ...
+Unpacking libtinfo-dev:amd64 (6.0+20160319-1) ...
+Selecting previously unselected package libncurses5-dev:amd64.
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_amd64.deb ...
+Unpacking libncurses5-dev:amd64 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-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) ...
+Preparing to unpack .../tabix_1.3.1-1_amd64.deb ...
+Unpacking tabix (1.3.1-1) ...
+Selecting previously unselected package zlib1g-dev:amd64.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
+Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-samtools-dummy.
Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:amd64 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
+Setting up libpipeline1: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 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 libunistring0:amd64 (0.9.3-5.2+b1) ...
+Setting up libssl1.0.2:amd64 (1.0.2g-2) ...
+Setting up libmagic1:amd64 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
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 libnettle6:amd64 (3.2-1) ...
+Setting up libhogweed4:amd64 (3.2-1) ...
+Setting up libidn11:amd64 (1.32-3) ...
+Setting up libffi6:amd64 (3.2.1-4) ...
+Setting up libp11-kit0:amd64 (0.23.2-3) ...
+Setting up libtasn1-6:amd64 (4.8-1) ...
+Setting up libgnutls30:amd64 (3.4.11-3) ...
+Setting up libkeyutils1:amd64 (1.5.9-8) ...
+Setting up libkrb5support0:amd64 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:amd64 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:amd64 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:amd64 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:amd64 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:amd64 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:amd64 (2.4.42+dfsg-2+b2) ...
+Setting up libicu55:amd64 (55.1-7) ...
+Setting up libxml2:amd64 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:amd64 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:amd64 (2.48.0-1) ...
No schema files found: doing nothing.
-Setting up libcroco3:arm64 (0.6.11-1) ...
+Setting up libcroco3:amd64 (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:arm64 (1.3-1) ...
-Setting up libhts-dev:arm64 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:amd64 (1.9.2-1) ...
+Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:amd64 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:amd64 (7.47.0-1) ...
+Setting up libhts1:amd64 (1.3.1-1) ...
+Setting up libhts-dev:amd64 (1.3.1-1) ...
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 (1.3-1) ...
-Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up libtinfo-dev:amd64 (6.0+20160319-1) ...
+Setting up libncurses5-dev:amd64 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
+Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [...]
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -398,28 +520,28 @@ 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
-SCHROOT_ALIAS_NAME=sid-arm64-sbuild
-SCHROOT_CHROOT_NAME=sid-arm64-sbuild
+SCHROOT_ALIAS_NAME=sid-amd64-sbuild
+SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-arm64-sbuild-bf008829-8b2e-4b88-8f01-d86db0e37341
+SCHROOT_SESSION_ID=sid-amd64-sbuild-1f3b6367-0ff9-4b46-bd25-d245123de362
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=c28742
+XDG_SESSION_ID=1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
-dpkg-buildpackage: host architecture arm64
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --before-build samtools-1.3.1
+dpkg-buildpackage: host architecture amd64
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -466,17 +588,17 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
+ ./configure --build=x86_64-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/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-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
@@ -486,6 +608,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -506,80 +630,80 @@ dh_auto_build -- \
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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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/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 -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -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 -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 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 -I. -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 -I. -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 -I. -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/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/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_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/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
@@ -589,40 +713,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j8 test BGZIP=/usr/bin/bgzip
+ make -j8 test VERBOSE=1 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/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/88o2zqM4pt/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/88o2zqM4pt/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/88o2zqM4pt/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/88o2zqM4pt/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -630,7 +754,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/T7B8QfZdHH/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/88o2zqM4pt/dict.fa.gz
.. ok
test_dict:
@@ -638,17 +762,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/T7B8QfZdHH/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/88o2zqM4pt/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/88o2zqM4pt/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/88o2zqM4pt/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -656,35 +780,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.bam.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/88o2zqM4pt/mpileup.bam.list -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/88o2zqM4pt/mpileup.cram.list -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/88o2zqM4pt/mpileup.bam.list -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/88o2zqM4pt/mpileup.cram.list -f /tmp/88o2zqM4pt/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/88o2zqM4pt/mpileup.cram.list -f /tmp/88o2zqM4pt/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/88o2zqM4pt/mpileup.cram.list -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/88o2zqM4pt/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/88o2zqM4pt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/88o2zqM4pt/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -934,41 +1058,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/88o2zqM4pt/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/88o2zqM4pt/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/88o2zqM4pt/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/88o2zqM4pt/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/88o2zqM4pt/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/88o2zqM4pt/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/88o2zqM4pt/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/88o2zqM4pt/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -982,419 +1106,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
+
+ 78: Count -l Library 3 (CRAM input) .. ok
+
+ 79: Filter -q 50 (SAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 140: Region Z (BAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 141: Count Z (BAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 267: Make CRAM with no UR field .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 263: CIGAR B-operator removal .. ok
+ 269: CIGAR B-operator removal .. ok
- 264: Big SAM -> BAM .. ok
+ 270: Big SAM -> BAM .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 267: Big SAM -> CRAM .. ok
+ 273: Big SAM -> CRAM .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 280: Subsample 0.5 (BAM input) ............ ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 281: Subsample 0.8 (BAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 282: Subsample 0.2 (CRAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 283: Subsample 0.5 (CRAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1542,7 +1678,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/2wJy_SzHz1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/VZvh0N2r5e - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1562,15 +1698,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/88o2zqM4pt/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/88o2zqM4pt/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/88o2zqM4pt/sorttmp
.. ok
test_fixmate:
@@ -1624,8 +1760,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1673,10 +1819,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1686,12 +1832,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1773,7 +1916,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1790,47 +1933,47 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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/aarch64-linux-gnu/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/lib/x86_64-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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/ca25e715d873602b77157e9025f3603731a07f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/ca25e715d873602b77157e9025f3603731a07f.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ac/ca25e715d873602b77157e9025f3603731a07f.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/16
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/16/d0d8c0a2fc793116231c27b0a2cb49901aca43.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/16/d0d8c0a2fc793116231c27b0a2cb49901aca43.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/16/d0d8c0a2fc793116231c27b0a2cb49901aca43.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/dbad36bcb006e1e9a5aa8dcb118401aa38c91c.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/dbad36bcb006e1e9a5aa8dcb118401aa38c91c.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/72/dbad36bcb006e1e9a5aa8dcb118401aa38c91c.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/0decbba75b095f594b97dd62096831e986b5d1.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/0decbba75b095f594b97dd62096831e986b5d1.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/0decbba75b095f594b97dd62096831e986b5d1.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/3df138a824b641561b5b8dc4b7e45276208d87.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/3df138a824b641561b5b8dc4b7e45276208d87.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/3df138a824b641561b5b8dc4b7e45276208d87.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f/11397c41d12d74c72c884c4603875132dbe68e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f/11397c41d12d74c72c884c4603875132dbe68e.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f/11397c41d12d74c72c884c4603875132dbe68e.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/79c45c29758a77753dd96e11f0fbf1f4cb5e83.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/79c45c29758a77753dd96e11f0fbf1f4cb5e83.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/ac/11149395c356ea0d209051e23aef8587486df8.debug debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/79c45c29758a77753dd96e11f0fbf1f4cb5e83.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
@@ -1838,14 +1981,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools 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/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 -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=0c0decbba75b095f594b97dd62096831e986b5d1 16d0d8c0a2fc793116231c27b0a2cb49901aca43 443df138a824b641561b5b8dc4b7e452 [...]
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
@@ -1864,17 +2006,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_arm64.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_amd64.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_arm64.deb'.
- dpkg-genchanges -B -marm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org> >../samtools_1.3-1_arm64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_amd64.deb'.
+ dpkg-genchanges -B -mamd64/i386 Build Daemon (babin) <buildd-babin at buildd.debian.org> >../samtools_1.3.1-1_amd64.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1630
+Build finished at 20160426-1231
Finished
────────
@@ -1891,108 +2033,100 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_arm64.changes:
-─────────────────────────────
+samtools_1.3.1-1_amd64.changes:
+───────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
-Architecture: arm64
-Version: 1.3-1
+Architecture: amd64
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: arm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: amd64/i386 Build Daemon (babin) <buildd-babin at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 5bcb890c9467c769b4fa4d446e2eeff9e098c857 466886 samtools-dbgsym_1.3-1_arm64.deb
- 55dd09f94f63a2c7a290fb3556fae1d19e0d4721 224754 samtools_1.3-1_arm64.deb
+ f8dda3a875805133363e5c83193fea2f531331b6 475662 samtools-dbgsym_1.3.1-1_amd64.deb
+ dc375a493d50d2d53526155935a95aff01f368fc 250438 samtools_1.3.1-1_amd64.deb
Checksums-Sha256:
- 7a2b90814726203831c3addac0744e4cc5c0a53b8bd5556e055424d2d31e05c7 466886 samtools-dbgsym_1.3-1_arm64.deb
- 4720931bb49f384c8f0c053a46495eed78d4c655532bc7174906e85c7f8b12ee 224754 samtools_1.3-1_arm64.deb
+ 6d5e383c0f163c3b407b817e689686e9b23b3b243023986fb9a6fddd44b8c953 475662 samtools-dbgsym_1.3.1-1_amd64.deb
+ 627e31834a20461150410abd920aa1108d72da68228c451b174c3a8f2b8b4637 250438 samtools_1.3.1-1_amd64.deb
Files:
- c5a0005797ff6bc6e7fea7f9c0c581d7 466886 debug extra samtools-dbgsym_1.3-1_arm64.deb
- 9310bf86b11396e1cbf179a3ed4001db 224754 science optional samtools_1.3-1_arm64.deb
+ 4f0d693c1abbd3ce070d740619b3b1e0 475662 debug extra samtools-dbgsym_1.3.1-1_amd64.deb
+ 4efbe88a1d084e6351f8a113e61d537a 250438 science optional samtools_1.3.1-1_amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_arm64.deb
-───────────────────────────────
+samtools-dbgsym_1.3.1-1_amd64.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 466886 bytes: control archive=817 bytes.
- 646 bytes, 13 lines control
+ size 475662 bytes: control archive=818 bytes.
+ 650 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
- Architecture: arm64
+ Version: 1.3.1-1
+ Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 552
- Depends: samtools (= 1.3-1)
+ Installed-Size: 547
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-────────────────────────
+ Build-Ids: 0c0decbba75b095f594b97dd62096831e986b5d1 16d0d8c0a2fc793116231c27b0a2cb49901aca43 443df138a824b641561b5b8dc4b7e45276208d87 5f11397c41d12d74c72c884c4603875132dbe68e 72dbad36bcb006e1e9a5aa8dcb118401aa38c91c acca25e715d873602b77157e9025f3603731a07f b879c45c29758a77753dd96e11f0fbf1f4cb5e83
+
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/0c/
+-rw-r--r-- root/root 11832 2016-04-26 12:31 ./usr/lib/debug/.build-id/0c/0decbba75b095f594b97dd62096831e986b5d1.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/16/
+-rw-r--r-- root/root 9136 2016-04-26 12:31 ./usr/lib/debug/.build-id/16/d0d8c0a2fc793116231c27b0a2cb49901aca43.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/44/
+-rw-r--r-- root/root 11832 2016-04-26 12:31 ./usr/lib/debug/.build-id/44/3df138a824b641561b5b8dc4b7e45276208d87.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/5f/
+-rw-r--r-- root/root 20768 2016-04-26 12:31 ./usr/lib/debug/.build-id/5f/11397c41d12d74c72c884c4603875132dbe68e.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/72/
+-rw-r--r-- root/root 11832 2016-04-26 12:31 ./usr/lib/debug/.build-id/72/dbad36bcb006e1e9a5aa8dcb118401aa38c91c.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/ac/
+-rw-r--r-- root/root 19920 2016-04-26 12:31 ./usr/lib/debug/.build-id/ac/ca25e715d873602b77157e9025f3603731a07f.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/lib/debug/.build-id/b8/
+-rw-r--r-- root/root 455552 2016-04-26 12:31 ./usr/lib/debug/.build-id/b8/79c45c29758a77753dd96e11f0fbf1f4cb5e83.debug
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 12:31 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_amd64.deb
+──────────────────────────
new debian package, version 2.0.
- size 224754 bytes: control archive=1634 bytes.
+ size 250438 bytes: control archive=1633 bytes.
807 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
- Architecture: arm64
+ Version: 1.3.1-1
+ Architecture: amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 664
- Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 715
+ Depends: libc6 (>= 2.14), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2005,48 +2139,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/bin/
+-rwxr-xr-x root/root 22856 2016-04-26 12:31 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10536 2016-04-26 12:31 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10536 2016-04-26 12:31 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10576 2016-04-26 12:31 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10504 2016-04-26 12:31 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 430368 2016-04-26 12:31 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22944 2016-04-26 12:31 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 12:31 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 12:31 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 12:31 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 12:31 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 12:31 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2065,24 +2199,24 @@ Not cleaning session: cloned chroot in use
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Build Architecture: arm64
-Build-Space: 16820
-Build-Time: 698
+Build Architecture: amd64
+Build-Space: 16984
+Build-Time: 116
Distribution: sid
-Host Architecture: arm64
-Install-Time: 25
-Job: samtools_1.3-1
-Machine Architecture: armhf
+Host Architecture: amd64
+Install-Time: 17
+Job: samtools_1.3.1-1
+Machine Architecture: amd64
Package: samtools
-Package-Time: 768
-Source-Version: 1.3-1
-Space: 16820
+Package-Time: 154
+Source-Version: 1.3.1-1
+Space: 16984
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160426-1231
+Build needed 00:02:34, 16984k disc space
+Signature with key 'A6BA9F19' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_amd64.changes A6BA9F19
Successfully signed changes file
diff --git a/arm64.log b/arm64.log
index 0d79756..d0c7638 100644
--- a/arm64.log
+++ b/arm64.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-linaro-03.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-arm-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (arm64) 05 Feb 2016 16:17 ║
+║ samtools 1.3.1-1 (arm64) 26 Apr 2016 12:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
-Machine Architecture: armhf
+Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-Ek4crO/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-Ek4crO' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-b71c62fa-a91b-4ec4-aae2-9abce6110116' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://mirror.bytemark.co.uk/debian unstable InRelease [196 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://mirror.bytemark.co.uk/debian unstable/main Sources [6767 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main arm64 Packages [122 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib arm64 Packages [2288 B]
+Get:10 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:11 http://mirror.bytemark.co.uk/debian unstable/contrib Sources [48.6 kB]
+Get:12 http://mirror.bytemark.co.uk/debian unstable/non-free Sources [84.1 kB]
+Get:13 http://mirror.bytemark.co.uk/debian unstable/main arm64 Packages [6816 kB]
+Get:14 http://mirror.bytemark.co.uk/debian unstable/contrib arm64 Packages [41.3 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main arm64 Packages [6816 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib arm64 Packages [41.3 kB]
+Fetched 28.2 MB in 17s (1611 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,46 +52,42 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 14s (261 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 1s (3254 kB/s)
Download complete and in download only mode
Check architectures
───────────────────
-sh: 1: gcc: not found
-sbuild: warning: couldn't determine gcc system type, falling back to default (native compilation)
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-SmTVOu/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-8n5Z9R/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-8n5Z9R/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-8n5Z9R/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 +102,28 @@ 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 10 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 19 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-SmTVOu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-8n5Z9R/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 ... 12179 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 ... 12232 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 (>= 4:5.3), 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-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]
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-J5Ui7B/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ Packages [747 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +137,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 19 not upgraded.
+Need to get 24.4 MB/24.4 MB of archives.
+After this operation, 87.3 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-J5Ui7B/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [990 B]
+Get:2 http://mirror.bytemark.co.uk/debian unstable/main arm64 bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://mirror.bytemark.co.uk/debian unstable/main arm64 groff-base arm64 1.22.3-7 [1156 kB]
+Get:4 http://mirror.bytemark.co.uk/debian unstable/main arm64 libbsd0 arm64 0.8.3-1 [77.8 kB]
+Get:5 http://mirror.bytemark.co.uk/debian unstable/main arm64 bsdmainutils arm64 9.0.10 [179 kB]
+Get:6 http://mirror.bytemark.co.uk/debian unstable/main arm64 libpipeline1 arm64 1.4.1-2 [25.0 kB]
+Get:7 http://mirror.bytemark.co.uk/debian unstable/main arm64 man-db arm64 2.7.5-1 [975 kB]
+Get:8 http://mirror.bytemark.co.uk/debian unstable/main arm64 autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://mirror.bytemark.co.uk/debian unstable/main arm64 libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
+Get:10 http://mirror.bytemark.co.uk/debian unstable/main arm64 libssl1.0.2 arm64 1.0.2g-2 [889 kB]
+Get:11 http://mirror.bytemark.co.uk/debian unstable/main arm64 libmagic1 arm64 1:5.25-2 [248 kB]
+Get:12 http://mirror.bytemark.co.uk/debian unstable/main arm64 file arm64 1:5.25-2 [61.5 kB]
+Get:13 http://mirror.bytemark.co.uk/debian unstable/main arm64 gettext-base arm64 0.19.7-2 [112 kB]
+Get:14 http://mirror.bytemark.co.uk/debian unstable/main arm64 libnettle6 arm64 3.2-1 [194 kB]
+Get:15 http://mirror.bytemark.co.uk/debian unstable/main arm64 libhogweed4 arm64 3.2-1 [128 kB]
+Get:16 http://mirror.bytemark.co.uk/debian unstable/main arm64 libidn11 arm64 1.32-3 [110 kB]
+Get:17 http://mirror.bytemark.co.uk/debian unstable/main arm64 libffi6 arm64 3.2.1-4 [18.9 kB]
+Get:18 http://mirror.bytemark.co.uk/debian unstable/main arm64 libp11-kit0 arm64 0.23.2-3 [88.2 kB]
+Get:19 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtasn1-6 arm64 4.8-1 [44.4 kB]
+Get:20 http://mirror.bytemark.co.uk/debian unstable/main arm64 libgnutls30 arm64 3.4.11-3 [683 kB]
+Get:21 http://mirror.bytemark.co.uk/debian unstable/main arm64 libkeyutils1 arm64 1.5.9-8 [11.6 kB]
+Get:22 http://mirror.bytemark.co.uk/debian unstable/main arm64 libkrb5support0 arm64 1.13.2+dfsg-5 [57.1 kB]
+Get:23 http://mirror.bytemark.co.uk/debian unstable/main arm64 libk5crypto3 arm64 1.13.2+dfsg-5 [106 kB]
+Get:24 http://mirror.bytemark.co.uk/debian unstable/main arm64 libkrb5-3 arm64 1.13.2+dfsg-5 [262 kB]
+Get:25 http://mirror.bytemark.co.uk/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.13.2+dfsg-5 [130 kB]
+Get:26 http://mirror.bytemark.co.uk/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.26.dfsg1-15 [65.4 kB]
+Get:27 http://mirror.bytemark.co.uk/debian unstable/main arm64 libsasl2-2 arm64 2.1.26.dfsg1-15 [96.1 kB]
+Get:28 http://mirror.bytemark.co.uk/debian unstable/main arm64 libldap-2.4-2 arm64 2.4.42+dfsg-2+b2 [198 kB]
+Get:29 http://mirror.bytemark.co.uk/debian unstable/main arm64 libicu55 arm64 55.1-7 [7492 kB]
+Get:30 http://mirror.bytemark.co.uk/debian unstable/main arm64 libxml2 arm64 2.9.3+dfsg1-1 [785 kB]
+Get:31 http://mirror.bytemark.co.uk/debian unstable/main arm64 libsigsegv2 arm64 2.10-5 [28.2 kB]
+Get:32 http://mirror.bytemark.co.uk/debian unstable/main arm64 m4 arm64 1.4.17-5 [244 kB]
+Get:33 http://mirror.bytemark.co.uk/debian unstable/main arm64 autoconf all 2.69-10 [338 kB]
+Get:34 http://mirror.bytemark.co.uk/debian unstable/main arm64 autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://mirror.bytemark.co.uk/debian unstable/main arm64 automake all 1:1.15-4 [735 kB]
+Get:36 http://mirror.bytemark.co.uk/debian unstable/main arm64 autopoint all 0.19.7-2 [424 kB]
+Get:37 http://mirror.bytemark.co.uk/debian unstable/main arm64 libglib2.0-0 arm64 2.48.0-1 [2508 kB]
+Get:38 http://mirror.bytemark.co.uk/debian unstable/main arm64 libcroco3 arm64 0.6.11-1 [128 kB]
+Get:39 http://mirror.bytemark.co.uk/debian unstable/main arm64 gettext arm64 0.19.7-2 [1411 kB]
+Get:40 http://mirror.bytemark.co.uk/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://mirror.bytemark.co.uk/debian unstable/main arm64 po-debconf all 1.0.19 [249 kB]
+Get:42 http://mirror.bytemark.co.uk/debian unstable/main arm64 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://mirror.bytemark.co.uk/debian unstable/main arm64 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://mirror.bytemark.co.uk/debian unstable/main arm64 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://mirror.bytemark.co.uk/debian unstable/main arm64 dh-autoreconf all 12 [15.8 kB]
+Get:48 http://mirror.bytemark.co.uk/debian unstable/main arm64 debhelper all 9.20160403 [800 kB]
+Get:49 http://mirror.bytemark.co.uk/debian unstable/main arm64 libnghttp2-14 arm64 1.9.2-1 [66.2 kB]
+Get:50 http://mirror.bytemark.co.uk/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d-1+b1 [53.8 kB]
+Get:51 http://mirror.bytemark.co.uk/debian unstable/main arm64 libssh2-1 arm64 1.5.0-2.1 [121 kB]
+Get:52 http://mirror.bytemark.co.uk/debian unstable/main arm64 libcurl3-gnutls arm64 7.47.0-1 [238 kB]
+Get:53 http://mirror.bytemark.co.uk/debian unstable/main arm64 libhts1 arm64 1.3.1-1 [215 kB]
+Get:54 http://mirror.bytemark.co.uk/debian unstable/main arm64 libhts-dev arm64 1.3.1-1 [285 kB]
+Get:55 http://mirror.bytemark.co.uk/debian unstable/main arm64 libio-pty-perl arm64 1:1.08-1.1+b1 [32.3 kB]
+Get:56 http://mirror.bytemark.co.uk/debian unstable/main arm64 libtinfo-dev arm64 6.0+20160319-1 [71.4 kB]
+Get:57 http://mirror.bytemark.co.uk/debian unstable/main arm64 libncurses5-dev arm64 6.0+20160319-1 [245 kB]
+Get:58 http://mirror.bytemark.co.uk/debian unstable/main arm64 tabix arm64 1.3.1-1 [212 kB]
+Get:59 http://mirror.bytemark.co.uk/debian unstable/main arm64 zlib1g-dev arm64 1:1.2.8.dfsg-2+b1 [200 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 20.0 MB in 6s (3012 kB/s)
+Fetched 24.4 MB in 4s (5315 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
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(Reading database ... 12232 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_arm64.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:arm64.
+Preparing to unpack .../libbsd0_0.8.3-1_arm64.deb ...
+Unpacking libbsd0:arm64 (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_arm64.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_arm64.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../libpipeline1_1.4.1-2_arm64.deb ...
Unpacking libpipeline1:arm64 (1.4.1-2) ...
@@ -224,12 +255,12 @@ 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) ...
+Selecting previously unselected package libssl1.0.2:arm64.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_arm64.deb ...
+Unpacking libssl1.0.2:arm64 (1.0.2g-2) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../libmagic1_1%3a5.25-2_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.25-2) ...
@@ -239,30 +270,78 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_arm64.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:arm64.
+Preparing to unpack .../libnettle6_3.2-1_arm64.deb ...
+Unpacking libnettle6:arm64 (3.2-1) ...
+Selecting previously unselected package libhogweed4:arm64.
+Preparing to unpack .../libhogweed4_3.2-1_arm64.deb ...
+Unpacking libhogweed4:arm64 (3.2-1) ...
+Selecting previously unselected package libidn11:arm64.
+Preparing to unpack .../libidn11_1.32-3_arm64.deb ...
+Unpacking libidn11:arm64 (1.32-3) ...
+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 libp11-kit0:arm64.
+Preparing to unpack .../libp11-kit0_0.23.2-3_arm64.deb ...
+Unpacking libp11-kit0:arm64 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:arm64.
+Preparing to unpack .../libtasn1-6_4.8-1_arm64.deb ...
+Unpacking libtasn1-6:arm64 (4.8-1) ...
+Selecting previously unselected package libgnutls30:arm64.
+Preparing to unpack .../libgnutls30_3.4.11-3_arm64.deb ...
+Unpacking libgnutls30:arm64 (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:arm64.
+Preparing to unpack .../libkeyutils1_1.5.9-8_arm64.deb ...
+Unpacking libkeyutils1:arm64 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:arm64.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_arm64.deb ...
+Unpacking libkrb5support0:arm64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:arm64.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_arm64.deb ...
+Unpacking libk5crypto3:arm64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:arm64.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_arm64.deb ...
+Unpacking libkrb5-3:arm64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:arm64.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_arm64.deb ...
+Unpacking libgssapi-krb5-2:arm64 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:arm64.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_arm64.deb ...
+Unpacking libsasl2-modules-db:arm64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:arm64.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_arm64.deb ...
+Unpacking libsasl2-2:arm64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:arm64.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_arm64.deb ...
+Unpacking libldap-2.4-2:arm64 (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:arm64.
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 libsigsegv2:arm64.
+Preparing to unpack .../libsigsegv2_2.10-5_arm64.deb ...
+Unpacking libsigsegv2:arm64 (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:arm64.
-Preparing to unpack .../libglib2.0-0_2.46.2-3_arm64.deb ...
-Unpacking libglib2.0-0:arm64 (2.46.2-3) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_arm64.deb ...
+Unpacking libglib2.0-0:arm64 (2.48.0-1) ...
Selecting previously unselected package libcroco3:arm64.
Preparing to unpack .../libcroco3_0.6.11-1_arm64.deb ...
Unpacking libcroco3:arm64 (0.6.11-1) ...
@@ -276,96 +355,137 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:arm64.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_arm64.deb ...
+Unpacking libnghttp2-14:arm64 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:arm64.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_arm64.deb ...
+Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:arm64.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_arm64.deb ...
+Unpacking libssh2-1:arm64 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:arm64.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_arm64.deb ...
+Unpacking libcurl3-gnutls:arm64 (7.47.0-1) ...
Selecting previously unselected package libhts1:arm64.
-Preparing to unpack .../libhts1_1.3-1_arm64.deb ...
-Unpacking libhts1:arm64 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_arm64.deb ...
+Unpacking libhts1:arm64 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:arm64.
-Preparing to unpack .../libhts-dev_1.3-1_arm64.deb ...
-Unpacking libhts-dev:arm64 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_arm64.deb ...
+Unpacking libhts-dev:arm64 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:arm64.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_arm64.deb ...
-Unpacking libtinfo-dev:arm64 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_arm64.deb ...
+Unpacking libtinfo-dev:arm64 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_arm64.deb ...
+Unpacking libncurses5-dev:arm64 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_arm64.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_arm64.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:arm64 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:arm64 (1.0.2g-2) ...
Setting up libmagic1:arm64 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:arm64 (3.2-1) ...
+Setting up libhogweed4:arm64 (3.2-1) ...
+Setting up libidn11:arm64 (1.32-3) ...
+Setting up libffi6:arm64 (3.2.1-4) ...
+Setting up libp11-kit0:arm64 (0.23.2-3) ...
+Setting up libtasn1-6:arm64 (4.8-1) ...
+Setting up libgnutls30:arm64 (3.4.11-3) ...
+Setting up libkeyutils1:arm64 (1.5.9-8) ...
+Setting up libkrb5support0:arm64 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:arm64 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:arm64 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:arm64 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:arm64 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:arm64 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:arm64 (2.4.42+dfsg-2+b2) ...
Setting up libicu55:arm64 (55.1-7) ...
Setting up libxml2:arm64 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:arm64 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:arm64 (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:arm64 (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:arm64 (1.3-1) ...
-Setting up libhts-dev:arm64 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:arm64 (1.9.2-1) ...
+Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:arm64 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:arm64 (7.47.0-1) ...
+Setting up libhts1:arm64 (1.3.1-1) ...
+Setting up libhts-dev:arm64 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:arm64 (6.0+20160319-1) ...
+Setting up libncurses5-dev:arm64 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [...]
+Kernel: Linux 3.16.0-4-arm64 arm64 (aarch64)
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_6.0.1-2 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +496,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -394,7 +514,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=8
+DEB_BUILD_OPTIONS=parallel=6
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
@@ -403,23 +523,23 @@ SCHROOT_CHROOT_NAME=sid-arm64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-arm64-sbuild-bf008829-8b2e-4b88-8f01-d86db0e37341
+SCHROOT_SESSION_ID=sid-arm64-sbuild-b71c62fa-a91b-4ec4-aae2-9abce6110116
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=c28742
+XDG_SESSION_ID=c19776
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture arm64
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -427,7 +547,7 @@ dh clean --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
touch config.mk
dh_auto_clean --
- make -j8 distclean
+ make -j6 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
@@ -466,15 +586,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -486,6 +606,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,84 +626,84 @@ dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(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 -j6 "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/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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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/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_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 -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_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
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
@@ -589,40 +711,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j8 test BGZIP=/usr/bin/bgzip
+ make -j6 test VERBOSE=1 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/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/dTMm_ENi0w/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/dTMm_ENi0w/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/T7B8QfZdHH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/dTMm_ENi0w/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/T7B8QfZdHH/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/dTMm_ENi0w/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -630,7 +752,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/T7B8QfZdHH/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/dTMm_ENi0w/dict.fa.gz
.. ok
test_dict:
@@ -638,17 +760,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/T7B8QfZdHH/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/dTMm_ENi0w/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/dTMm_ENi0w/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/T7B8QfZdHH/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/dTMm_ENi0w/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -656,35 +778,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.bam.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/dTMm_ENi0w/mpileup.bam.list -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/dTMm_ENi0w/mpileup.cram.list -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/dTMm_ENi0w/mpileup.bam.list -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/dTMm_ENi0w/mpileup.cram.list -f /tmp/dTMm_ENi0w/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/dTMm_ENi0w/mpileup.cram.list -f /tmp/dTMm_ENi0w/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/T7B8QfZdHH/mpileup.cram.list -f /tmp/T7B8QfZdHH/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/dTMm_ENi0w/mpileup.cram.list -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/dTMm_ENi0w/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/dTMm_ENi0w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/dTMm_ENi0w/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -934,41 +1056,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/dTMm_ENi0w/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/dTMm_ENi0w/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/dTMm_ENi0w/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/dTMm_ENi0w/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/dTMm_ENi0w/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/dTMm_ENi0w/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/T7B8QfZdHH/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/dTMm_ENi0w/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/T7B8QfZdHH/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/dTMm_ENi0w/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -982,419 +1104,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 74: Count -l Library 3 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 75: Filter -l Library 3 (BAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 76: Count -l Library 3 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 141: Count Z (BAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 264: Big SAM -> BAM .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 267: Big SAM -> CRAM .. ok
+ 267: Make CRAM with no UR field .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 270: Big SAM -> BAM .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 273: Big SAM -> CRAM .. ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
+
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1542,7 +1676,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/2wJy_SzHz1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/GUFjZoDVhq - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1562,15 +1696,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/dTMm_ENi0w/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/dTMm_ENi0w/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/T7B8QfZdHH/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/dTMm_ENi0w/sorttmp
.. ok
test_fixmate:
@@ -1624,8 +1758,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1673,10 +1817,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1686,12 +1830,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1721,7 +1862,7 @@ make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_install -- \
prefix=/usr
install -d debian/samtools
- make -j8 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
+ make -j6 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
@@ -1773,7 +1914,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1796,41 +1937,41 @@ 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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1/3b706a8c3a817614e4bbb8138a1c5bace88291.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1/3b706a8c3a817614e4bbb8138a1c5bace88291.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f1/3b706a8c3a817614e4bbb8138a1c5bace88291.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/c51fe757d40f867137e917aad66d3d4a3c5579.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/c51fe757d40f867137e917aad66d3d4a3c5579.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f2/c51fe757d40f867137e917aad66d3d4a3c5579.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/fa8ebbf20336d773dfaa7f42cd6d30b9384608.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/fa8ebbf20336d773dfaa7f42cd6d30b9384608.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/fa8ebbf20336d773dfaa7f42cd6d30b9384608.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/56
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/56/02cbdd9ba65a37d9011f70d729f86b4cb0f647.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/56/02cbdd9ba65a37d9011f70d729f86b4cb0f647.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/56/02cbdd9ba65a37d9011f70d729f86b4cb0f647.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/d44b866bbec57dc9089be5a2ee12afdfefe2cb.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/d44b866bbec57dc9089be5a2ee12afdfefe2cb.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a9/d44b866bbec57dc9089be5a2ee12afdfefe2cb.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/005f8f18bde1c6d632ff6e77a252b2af57d25b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/005f8f18bde1c6d632ff6e77a252b2af57d25b.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/28/005f8f18bde1c6d632ff6e77a252b2af57d25b.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/85
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/85/f60d3dcfc51e12c64b4d60cebb29613c72347f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/85/f60d3dcfc51e12c64b4d60cebb29613c72347f.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/ac/11149395c356ea0d209051e23aef8587486df8.debug debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/85/f60d3dcfc51e12c64b4d60cebb29613c72347f.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
@@ -1838,14 +1979,14 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short 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/ace2sam debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim 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/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 -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=28005f8f18bde1c6d632ff6e77a252b2af57d25b 5602cbdd9ba65a37d9011f70d729f86b4cb0f647 85f60d3dcfc51e12c64b4d60cebb2961 [...]
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
@@ -1864,17 +2005,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_arm64.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_arm64.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_arm64.deb'.
- dpkg-genchanges -B -marm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org> >../samtools_1.3-1_arm64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_arm64.deb'.
+ dpkg-genchanges -B -marm Build Daemon (arm-arm-01) <buildd_arm64-arm-arm-01 at buildd.debian.org> >../samtools_1.3.1-1_arm64.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1630
+Build finished at 20160426-1304
Finished
────────
@@ -1891,108 +2032,100 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_arm64.changes:
-─────────────────────────────
+samtools_1.3.1-1_arm64.changes:
+───────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: arm64
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: arm Build Daemon (arm-linaro-03) <buildd_arm64-arm-linaro-03 at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: arm Build Daemon (arm-arm-01) <buildd_arm64-arm-arm-01 at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 5bcb890c9467c769b4fa4d446e2eeff9e098c857 466886 samtools-dbgsym_1.3-1_arm64.deb
- 55dd09f94f63a2c7a290fb3556fae1d19e0d4721 224754 samtools_1.3-1_arm64.deb
+ 4b8071577561b1757729121f8b9e408ebe19e007 476114 samtools-dbgsym_1.3.1-1_arm64.deb
+ 1b5f4a31b999b7add1f73000b709a01390855f35 228464 samtools_1.3.1-1_arm64.deb
Checksums-Sha256:
- 7a2b90814726203831c3addac0744e4cc5c0a53b8bd5556e055424d2d31e05c7 466886 samtools-dbgsym_1.3-1_arm64.deb
- 4720931bb49f384c8f0c053a46495eed78d4c655532bc7174906e85c7f8b12ee 224754 samtools_1.3-1_arm64.deb
+ c3ab17bea66600e43887dd80de06cbc87e968c6c1107e3c65da3a4a8a803ef28 476114 samtools-dbgsym_1.3.1-1_arm64.deb
+ 3dc1ccbc5087d2f7b64a379d7546f8126d60793cdfb7c926fcfd5983bc75a4fa 228464 samtools_1.3.1-1_arm64.deb
Files:
- c5a0005797ff6bc6e7fea7f9c0c581d7 466886 debug extra samtools-dbgsym_1.3-1_arm64.deb
- 9310bf86b11396e1cbf179a3ed4001db 224754 science optional samtools_1.3-1_arm64.deb
+ 1d2eac858c266179ab8c85d646dedd4f 476114 debug extra samtools-dbgsym_1.3.1-1_arm64.deb
+ 32c6885cb5f308f6f2a27abc24259730 228464 science optional samtools_1.3.1-1_arm64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_arm64.deb
-───────────────────────────────
+samtools-dbgsym_1.3.1-1_arm64.deb
+─────────────────────────────────
new debian package, version 2.0.
- size 466886 bytes: control archive=817 bytes.
- 646 bytes, 13 lines control
+ size 476114 bytes: control archive=822 bytes.
+ 650 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 552
- Depends: samtools (= 1.3-1)
+ Installed-Size: 561
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-────────────────────────
+ Build-Ids: 28005f8f18bde1c6d632ff6e77a252b2af57d25b 5602cbdd9ba65a37d9011f70d729f86b4cb0f647 85f60d3dcfc51e12c64b4d60cebb29613c72347f 94fa8ebbf20336d773dfaa7f42cd6d30b9384608 a9d44b866bbec57dc9089be5a2ee12afdfefe2cb f13b706a8c3a817614e4bbb8138a1c5bace88291 f2c51fe757d40f867137e917aad66d3d4a3c5579
+
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/28/
+-rw-r--r-- root/root 21424 2016-04-26 13:04 ./usr/lib/debug/.build-id/28/005f8f18bde1c6d632ff6e77a252b2af57d25b.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/56/
+-rw-r--r-- root/root 13248 2016-04-26 13:04 ./usr/lib/debug/.build-id/56/02cbdd9ba65a37d9011f70d729f86b4cb0f647.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/85/
+-rw-r--r-- root/root 461888 2016-04-26 13:04 ./usr/lib/debug/.build-id/85/f60d3dcfc51e12c64b4d60cebb29613c72347f.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/94/
+-rw-r--r-- root/root 12968 2016-04-26 13:04 ./usr/lib/debug/.build-id/94/fa8ebbf20336d773dfaa7f42cd6d30b9384608.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/a9/
+-rw-r--r-- root/root 13272 2016-04-26 13:04 ./usr/lib/debug/.build-id/a9/d44b866bbec57dc9089be5a2ee12afdfefe2cb.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/f1/
+-rw-r--r-- root/root 22056 2016-04-26 13:04 ./usr/lib/debug/.build-id/f1/3b706a8c3a817614e4bbb8138a1c5bace88291.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/lib/debug/.build-id/f2/
+-rw-r--r-- root/root 10384 2016-04-26 13:04 ./usr/lib/debug/.build-id/f2/c51fe757d40f867137e917aad66d3d4a3c5579.debug
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 13:04 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_arm64.deb
+──────────────────────────
new debian package, version 2.0.
- size 224754 bytes: control archive=1634 bytes.
+ size 228464 bytes: control archive=1636 bytes.
807 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: arm64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 664
- Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 671
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2005,48 +2138,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/bin/
+-rwxr-xr-x root/root 18608 2016-04-26 13:04 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10392 2016-04-26 13:04 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10392 2016-04-26 13:04 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10424 2016-04-26 13:04 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10352 2016-04-26 13:04 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 385120 2016-04-26 13:04 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 26888 2016-04-26 13:04 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 13:04 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 13:04 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 13:04 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 13:04 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 13:04 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2066,23 +2199,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: arm64
-Build-Space: 16820
-Build-Time: 698
+Build-Space: 16928
+Build-Time: 1981
Distribution: sid
Host Architecture: arm64
-Install-Time: 25
-Job: samtools_1.3-1
-Machine Architecture: armhf
+Install-Time: 43
+Job: samtools_1.3.1-1
+Machine Architecture: arm64
Package: samtools
-Package-Time: 768
-Source-Version: 1.3-1
-Space: 16820
+Package-Time: 2083
+Source-Version: 1.3.1-1
+Space: 16928
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160426-1304
+Build needed 00:34:43, 16928k disc space
+Signature with key '8C88BE92' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_arm64.changes 8C88BE92
Successfully signed changes file
diff --git a/armel.log b/armel.log
index 520189f..602947f 100644
--- a/armel.log
+++ b/armel.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on henze.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on antheil.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (armel) 05 Feb 2016 17:15 ║
+║ samtools 1.3.1-1 (armel) 26 Apr 2016 14:07 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
-Machine Architecture: armhf
+Machine Architecture: armel
Host Architecture: armel
Build Architecture: armel
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-eMqIUL/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-eMqIUL' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-armel-sbuild-88e25465-34fe-4b6f-b44a-3c0d4deb75a0' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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 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)
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:2 http://ftp.uk.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [103 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/main armel Packages [110 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/contrib armel Packages [2284 B]
+Get:9 http://ftp.uk.debian.org/debian unstable/main Sources [6767 kB]
+Get:10 http://ftp.uk.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:11 http://ftp.uk.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:12 http://ftp.uk.debian.org/debian unstable/main armel Packages [6875 kB]
+Get:13 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:14 http://ftp.uk.debian.org/debian unstable/contrib armel Packages [42.2 kB]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main armel Packages [6875 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib armel Packages [42.2 kB]
+Fetched 28.3 MB in 13s (2131 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 (148 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (19.7 MB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,15 @@ 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-k1gxXu/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-9WrAA2/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ Packages [527 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +104,28 @@ 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 8 not upgraded.
-Need to get 0 B/770 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 18 not upgraded.
+Need to get 0 B/774 B of archives.
After this operation, 0 B of additional disk space will be used.
-Get:1 file:/«BUILDDIR»/resolver-k1gxXu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-9WrAA2/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [774 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
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(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.)
+(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%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12098 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 (>= 4:5.3), 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-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]
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-SzSW82/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ Packages [747 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +139,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 18 not upgraded.
+Need to get 24.2 MB/24.2 MB of archives.
+After this operation, 86.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-SzSW82/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [994 B]
+Get:2 http://ftp.uk.debian.org/debian unstable/main armel bash-completion all 1:2.1-4.3 [178 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:4 http://ftp.uk.debian.org/debian unstable/main armel libbsd0 armel 0.8.3-1 [86.4 kB]
+Get:5 http://ftp.uk.debian.org/debian unstable/main armel bsdmainutils armel 9.0.10 [179 kB]
+Get:6 http://ftp.uk.debian.org/debian unstable/main armel libpipeline1 armel 1.4.1-2 [23.6 kB]
+Get:7 http://ftp.uk.debian.org/debian unstable/main armel man-db armel 2.7.5-1 [977 kB]
+Get:8 http://ftp.uk.debian.org/debian unstable/main armel autoconf-archive all 20150925-1 [688 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]
+Get:10 http://ftp.uk.debian.org/debian unstable/main armel libssl1.0.2 armel 1.0.2g-2 [885 kB]
+Get:11 http://ftp.uk.debian.org/debian unstable/main armel libmagic1 armel 1:5.25-2 [252 kB]
+Get:12 http://ftp.uk.debian.org/debian unstable/main armel file armel 1:5.25-2 [61.1 kB]
+Get:13 http://ftp.uk.debian.org/debian unstable/main armel gettext-base armel 0.19.7-2 [111 kB]
+Get:14 http://ftp.uk.debian.org/debian unstable/main armel libnettle6 armel 3.2-1 [204 kB]
+Get:15 http://ftp.uk.debian.org/debian unstable/main armel libhogweed4 armel 3.2-1 [125 kB]
+Get:16 http://ftp.uk.debian.org/debian unstable/main armel libidn11 armel 1.32-3 [110 kB]
+Get:17 http://ftp.uk.debian.org/debian unstable/main armel libffi6 armel 3.2.1-4 [18.5 kB]
+Get:18 http://ftp.uk.debian.org/debian unstable/main armel libp11-kit0 armel 0.23.2-3 [93.3 kB]
+Get:19 http://ftp.uk.debian.org/debian unstable/main armel libtasn1-6 armel 4.8-1 [43.9 kB]
+Get:20 http://ftp.uk.debian.org/debian unstable/main armel libgnutls30 armel 3.4.11-3 [718 kB]
+Get:21 http://ftp.uk.debian.org/debian unstable/main armel libkeyutils1 armel 1.5.9-8 [11.4 kB]
+Get:22 http://ftp.uk.debian.org/debian unstable/main armel libkrb5support0 armel 1.13.2+dfsg-5 [56.6 kB]
+Get:23 http://ftp.uk.debian.org/debian unstable/main armel libk5crypto3 armel 1.13.2+dfsg-5 [111 kB]
+Get:24 http://ftp.uk.debian.org/debian unstable/main armel libkrb5-3 armel 1.13.2+dfsg-5 [261 kB]
+Get:25 http://ftp.uk.debian.org/debian unstable/main armel libgssapi-krb5-2 armel 1.13.2+dfsg-5 [130 kB]
+Get:26 http://ftp.uk.debian.org/debian unstable/main armel libsasl2-modules-db armel 2.1.26.dfsg1-15 [65.5 kB]
+Get:27 http://ftp.uk.debian.org/debian unstable/main armel libsasl2-2 armel 2.1.26.dfsg1-15 [96.4 kB]
+Get:28 http://ftp.uk.debian.org/debian unstable/main armel libldap-2.4-2 armel 2.4.42+dfsg-2+b2 [200 kB]
+Get:29 http://ftp.uk.debian.org/debian unstable/main armel libicu55 armel 55.1-7 [7340 kB]
+Get:30 http://ftp.uk.debian.org/debian unstable/main armel libxml2 armel 2.9.3+dfsg1-1 [803 kB]
+Get:31 http://ftp.uk.debian.org/debian unstable/main armel libsigsegv2 armel 2.10-5 [28.3 kB]
+Get:32 http://ftp.uk.debian.org/debian unstable/main armel m4 armel 1.4.17-5 [239 kB]
+Get:33 http://ftp.uk.debian.org/debian unstable/main armel autoconf all 2.69-10 [338 kB]
+Get:34 http://ftp.uk.debian.org/debian unstable/main armel autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://ftp.uk.debian.org/debian unstable/main armel automake all 1:1.15-4 [735 kB]
+Get:36 http://ftp.uk.debian.org/debian unstable/main armel autopoint all 0.19.7-2 [424 kB]
+Get:37 http://ftp.uk.debian.org/debian unstable/main armel libglib2.0-0 armel 2.48.0-1 [2547 kB]
+Get:38 http://ftp.uk.debian.org/debian unstable/main armel libcroco3 armel 0.6.11-1 [132 kB]
+Get:39 http://ftp.uk.debian.org/debian unstable/main armel gettext armel 0.19.7-2 [1406 kB]
+Get:40 http://ftp.uk.debian.org/debian unstable/main armel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://ftp.uk.debian.org/debian unstable/main armel po-debconf all 1.0.19 [249 kB]
+Get:42 http://ftp.uk.debian.org/debian unstable/main armel libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://ftp.uk.debian.org/debian unstable/main armel libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://ftp.uk.debian.org/debian unstable/main armel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://ftp.uk.debian.org/debian unstable/main armel dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://ftp.uk.debian.org/debian unstable/main armel libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://ftp.uk.debian.org/debian unstable/main armel dh-autoreconf all 12 [15.8 kB]
+Get:48 http://ftp.uk.debian.org/debian unstable/main armel debhelper all 9.20160403 [800 kB]
+Get:49 http://ftp.uk.debian.org/debian unstable/main armel libnghttp2-14 armel 1.9.2-1 [65.6 kB]
+Get:50 http://ftp.uk.debian.org/debian unstable/main armel librtmp1 armel 2.4+20151223.gitfa8646d-1+b1 [55.0 kB]
+Get:51 http://ftp.uk.debian.org/debian unstable/main armel libssh2-1 armel 1.5.0-2.1 [121 kB]
+Get:52 http://ftp.uk.debian.org/debian unstable/main armel libcurl3-gnutls armel 7.47.0-1 [244 kB]
+Get:53 http://ftp.uk.debian.org/debian unstable/main armel libhts1 armel 1.3.1-1 [216 kB]
+Get:54 http://ftp.uk.debian.org/debian unstable/main armel libhts-dev armel 1.3.1-1 [273 kB]
+Get:55 http://ftp.uk.debian.org/debian unstable/main armel libio-pty-perl armel 1:1.08-1.1+b1 [33.2 kB]
+Get:56 http://ftp.uk.debian.org/debian unstable/main armel libtinfo-dev armel 6.0+20160319-1 [66.3 kB]
+Get:57 http://ftp.uk.debian.org/debian unstable/main armel libncurses5-dev armel 6.0+20160319-1 [157 kB]
+Get:58 http://ftp.uk.debian.org/debian unstable/main armel tabix armel 1.3.1-1 [206 kB]
+Get:59 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 19.8 MB in 1s (17.1 MB/s)
+Fetched 24.2 MB in 1s (15.9 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12098 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_armel.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:armel.
+Preparing to unpack .../libbsd0_0.8.3-1_armel.deb ...
+Unpacking libbsd0:armel (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_armel.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_armel.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:armel.
Preparing to unpack .../libpipeline1_1.4.1-2_armel.deb ...
Unpacking libpipeline1:armel (1.4.1-2) ...
@@ -224,12 +257,12 @@ 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) ...
+Selecting previously unselected package libssl1.0.2:armel.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_armel.deb ...
+Unpacking libssl1.0.2:armel (1.0.2g-2) ...
Selecting previously unselected package libmagic1:armel.
Preparing to unpack .../libmagic1_1%3a5.25-2_armel.deb ...
Unpacking libmagic1:armel (1:5.25-2) ...
@@ -239,30 +272,78 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_armel.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:armel.
+Preparing to unpack .../libnettle6_3.2-1_armel.deb ...
+Unpacking libnettle6:armel (3.2-1) ...
+Selecting previously unselected package libhogweed4:armel.
+Preparing to unpack .../libhogweed4_3.2-1_armel.deb ...
+Unpacking libhogweed4:armel (3.2-1) ...
+Selecting previously unselected package libidn11:armel.
+Preparing to unpack .../libidn11_1.32-3_armel.deb ...
+Unpacking libidn11:armel (1.32-3) ...
+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 libp11-kit0:armel.
+Preparing to unpack .../libp11-kit0_0.23.2-3_armel.deb ...
+Unpacking libp11-kit0:armel (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:armel.
+Preparing to unpack .../libtasn1-6_4.8-1_armel.deb ...
+Unpacking libtasn1-6:armel (4.8-1) ...
+Selecting previously unselected package libgnutls30:armel.
+Preparing to unpack .../libgnutls30_3.4.11-3_armel.deb ...
+Unpacking libgnutls30:armel (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:armel.
+Preparing to unpack .../libkeyutils1_1.5.9-8_armel.deb ...
+Unpacking libkeyutils1:armel (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:armel.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_armel.deb ...
+Unpacking libkrb5support0:armel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:armel.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_armel.deb ...
+Unpacking libk5crypto3:armel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:armel.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_armel.deb ...
+Unpacking libkrb5-3:armel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:armel.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_armel.deb ...
+Unpacking libgssapi-krb5-2:armel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:armel.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_armel.deb ...
+Unpacking libsasl2-modules-db:armel (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:armel.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_armel.deb ...
+Unpacking libsasl2-2:armel (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:armel.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_armel.deb ...
+Unpacking libldap-2.4-2:armel (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:armel.
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 libsigsegv2:armel.
+Preparing to unpack .../libsigsegv2_2.10-5_armel.deb ...
+Unpacking libsigsegv2:armel (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:armel.
-Preparing to unpack .../libglib2.0-0_2.46.2-3_armel.deb ...
-Unpacking libglib2.0-0:armel (2.46.2-3) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_armel.deb ...
+Unpacking libglib2.0-0:armel (2.48.0-1) ...
Selecting previously unselected package libcroco3:armel.
Preparing to unpack .../libcroco3_0.6.11-1_armel.deb ...
Unpacking libcroco3:armel (0.6.11-1) ...
@@ -276,96 +357,137 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:armel.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_armel.deb ...
+Unpacking libnghttp2-14:armel (1.9.2-1) ...
+Selecting previously unselected package librtmp1:armel.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_armel.deb ...
+Unpacking librtmp1:armel (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:armel.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_armel.deb ...
+Unpacking libssh2-1:armel (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:armel.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_armel.deb ...
+Unpacking libcurl3-gnutls:armel (7.47.0-1) ...
Selecting previously unselected package libhts1:armel.
-Preparing to unpack .../libhts1_1.3-1_armel.deb ...
-Unpacking libhts1:armel (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_armel.deb ...
+Unpacking libhts1:armel (1.3.1-1) ...
Selecting previously unselected package libhts-dev:armel.
-Preparing to unpack .../libhts-dev_1.3-1_armel.deb ...
-Unpacking libhts-dev:armel (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_armel.deb ...
+Unpacking libhts-dev:armel (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:armel.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_armel.deb ...
-Unpacking libtinfo-dev:armel (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_armel.deb ...
+Unpacking libtinfo-dev:armel (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_armel.deb ...
+Unpacking libncurses5-dev:armel (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_armel.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_armel.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:armel (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:armel (1.0.2g-2) ...
Setting up libmagic1:armel (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:armel (3.2-1) ...
+Setting up libhogweed4:armel (3.2-1) ...
+Setting up libidn11:armel (1.32-3) ...
+Setting up libffi6:armel (3.2.1-4) ...
+Setting up libp11-kit0:armel (0.23.2-3) ...
+Setting up libtasn1-6:armel (4.8-1) ...
+Setting up libgnutls30:armel (3.4.11-3) ...
+Setting up libkeyutils1:armel (1.5.9-8) ...
+Setting up libkrb5support0:armel (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:armel (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:armel (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:armel (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:armel (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:armel (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:armel (2.4.42+dfsg-2+b2) ...
Setting up libicu55:armel (55.1-7) ...
Setting up libxml2:armel (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:armel (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:armel (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armel (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:armel (1.3-1) ...
-Setting up libhts-dev:armel (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:armel (1.9.2-1) ...
+Setting up librtmp1:armel (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:armel (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:armel (7.47.0-1) ...
+Setting up libhts1:armel (1.3.1-1) ...
+Setting up libhts-dev:armel (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:armel (6.0+20160319-1) ...
+Setting up libncurses5-dev:armel (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:armel (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [...]
+Kernel: Linux 3.16.0-4-armmp-lpae armel (armv7l)
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -394,7 +516,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=4
+DEB_BUILD_OPTIONS=parallel=1
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
@@ -403,31 +525,31 @@ SCHROOT_CHROOT_NAME=sid-armel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-armel-sbuild-d8a5be7c-0840-49b8-a74b-db6b5daa15ff
+SCHROOT_SESSION_ID=sid-armel-sbuild-88e25465-34fe-4b6f-b44a-3c0d4deb75a0
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=1
+XDG_SESSION_ID=482
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture armel
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
- dh_testdir -O--parallel
+ dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/«PKGBUILDDIR»'
touch config.mk
dh_auto_clean --
- make -j4 distclean
+ 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
@@ -438,7 +560,7 @@ 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
+ dh_clean
rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
@@ -466,15 +588,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -486,6 +608,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,125 +628,125 @@ 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 -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 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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
-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 -- \
BGZIP=/usr/bin/bgzip
- make -j4 test BGZIP=/usr/bin/bgzip
+ make -j1 test VERBOSE=1 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/Is7syFcP_X/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/OkB7P37CCO/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Is7syFcP_X/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/OkB7P37CCO/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Is7syFcP_X/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/OkB7P37CCO/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/Is7syFcP_X/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/OkB7P37CCO/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -630,7 +754,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/Is7syFcP_X/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/OkB7P37CCO/dict.fa.gz
.. ok
test_dict:
@@ -638,17 +762,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/Is7syFcP_X/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/OkB7P37CCO/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/Is7syFcP_X/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/OkB7P37CCO/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/Is7syFcP_X/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/OkB7P37CCO/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -656,35 +780,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/Is7syFcP_X/mpileup.bam.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/OkB7P37CCO/mpileup.bam.list -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/OkB7P37CCO/mpileup.cram.list -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/OkB7P37CCO/mpileup.bam.list -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/OkB7P37CCO/mpileup.cram.list -f /tmp/OkB7P37CCO/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/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/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/OkB7P37CCO/mpileup.cram.list -f /tmp/OkB7P37CCO/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/Is7syFcP_X/mpileup.cram.list -f /tmp/Is7syFcP_X/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/OkB7P37CCO/mpileup.cram.list -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OkB7P37CCO/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/OkB7P37CCO/mpileup.ref.fa.gz -r17:1050-1060 /tmp/OkB7P37CCO/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -934,41 +1058,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/Is7syFcP_X/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/OkB7P37CCO/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/Is7syFcP_X/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/OkB7P37CCO/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/Is7syFcP_X/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/OkB7P37CCO/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/Is7syFcP_X/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/OkB7P37CCO/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/OkB7P37CCO/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/OkB7P37CCO/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/Is7syFcP_X/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/OkB7P37CCO/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/Is7syFcP_X/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/OkB7P37CCO/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -982,419 +1106,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 75: Filter -l Library 3 (BAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 76: Count -l Library 3 (BAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 141: Count Z (BAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 264: Big SAM -> BAM .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 267: Make CRAM with no UR field .. ok
- 267: Big SAM -> CRAM .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 270: Big SAM -> BAM .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 273: Big SAM -> CRAM .. ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1542,7 +1678,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/TLzZ0vKq6c - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/8418B1NY1f - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1562,15 +1698,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/OkB7P37CCO/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/OkB7P37CCO/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/Is7syFcP_X/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/OkB7P37CCO/sorttmp
.. ok
test_fixmate:
@@ -1624,8 +1760,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1641,15 +1787,11 @@ test_reheader:
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:.*//'
-
- ERR:
-.. failed ...
+.. 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:.*//'
-
- ERR:
-.. failed ...
+.. ok
test_addrprg:
/«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
@@ -1677,29 +1819,375 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 396
- failed .. 2
- expected failure .. 18
+ total .. 423
+ passed .. 403
+ failed .. 0
+ expected failure .. 20
unexpected pass .. 0
-Makefile:201: recipe for target 'test' failed
-make[2]: *** [test] Error 1
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
+
+Expected passes: 124
+Unexpected passes: 0
+Expected failures: 0
+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
+test/split/test_parse_args
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
+ 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/
+ 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\.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
+ 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/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/dbgsym-root/usr/lib/debug/.build-id/5f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f/76211bbb973709cc9484f8b9c7c681dfb48a7b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5f/76211bbb973709cc9484f8b9c7c681dfb48a7b.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/5f/76211bbb973709cc9484f8b9c7c681dfb48a7b.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84/3f27d6956db8487122181beeea46ac7abb256f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/84/3f27d6956db8487122181beeea46ac7abb256f.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/84/3f27d6956db8487122181beeea46ac7abb256f.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/253512f9a4cff3a5eb697efe3b4fa35c7f6f42.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/253512f9a4cff3a5eb697efe3b4fa35c7f6f42.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/30/253512f9a4cff3a5eb697efe3b4fa35c7f6f42.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f/5836f54bcaf5171bd3e328d4462d0b920464f0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9f/5836f54bcaf5171bd3e328d4462d0b920464f0.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/9f/5836f54bcaf5171bd3e328d4462d0b920464f0.debug debian/samtools/usr/bin/maq2sam-short
+ 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-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8/e962b9c7ceb4a6972fdadb2b39287d53cc95c5.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e8/e962b9c7ceb4a6972fdadb2b39287d53cc95c5.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/e8/e962b9c7ceb4a6972fdadb2b39287d53cc95c5.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98/d23e12c93aece27c7123b64fbf3859e4ffbbb2.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/98/d23e12c93aece27c7123b64fbf3859e4ffbbb2.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/98/d23e12c93aece27c7123b64fbf3859e4ffbbb2.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/64
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/64/bda7cf8f30161939a7eb2c52903885df46351f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/64/bda7cf8f30161939a7eb2c52903885df46351f.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/64/bda7cf8f30161939a7eb2c52903885df46351f.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/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long were not linked against ld-linux.so.3 (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/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short 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/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=30253512f9a4cff3a5eb697efe3b4fa35c7f6f42 5f76211bbb973709cc9484f8b9c7c681dfb48a7b 64bda7cf8f30161939a7eb2c52903885 [...]
+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 ${perl:Depends}
+ chmod 0644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_armel.deb'.
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../samtools_1.3.1-1_armel.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1721
+Build finished at 20160426-1422
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.3.1-1_armel.changes:
+───────────────────────────────
+
+Format: 1.8
+Date: Tue, 26 Apr 2016 21:12:05 +0900
+Source: samtools
+Binary: samtools samtools-test
+Architecture: armel
+Version: 1.3.1-1
+Distribution: sid
+Urgency: medium
+Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Changes:
+ samtools (1.3.1-1) unstable; urgency=medium
+ .
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
+Checksums-Sha1:
+ c08f85930afba6bbb174a4af190ecf8dd5f1e4eb 453516 samtools-dbgsym_1.3.1-1_armel.deb
+ d7f995a869e928784064d4ef7a0eaf69e9008a95 220968 samtools_1.3.1-1_armel.deb
+Checksums-Sha256:
+ 5fcefce0057805204929b84bf9c4588482b6f7191201e3cb95fd9d409e475da2 453516 samtools-dbgsym_1.3.1-1_armel.deb
+ 033e475efd7c30a5629cba25f6ba547265f8c9211024b6d781f0ef5847344b40 220968 samtools_1.3.1-1_armel.deb
+Files:
+ 95a7ab76844067c4b73c747013d5a592 453516 debug extra samtools-dbgsym_1.3.1-1_armel.deb
+ 90149293de50f25fc833f1abf17396dc 220968 science optional samtools_1.3.1-1_armel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-dbgsym_1.3.1-1_armel.deb
+─────────────────────────────────
+
+ new debian package, version 2.0.
+ size 453516 bytes: control archive=820 bytes.
+ 650 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.3.1-1
+ Architecture: armel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 526
+ Depends: samtools (= 1.3.1-1)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 30253512f9a4cff3a5eb697efe3b4fa35c7f6f42 5f76211bbb973709cc9484f8b9c7c681dfb48a7b 64bda7cf8f30161939a7eb2c52903885df46351f 843f27d6956db8487122181beeea46ac7abb256f 98d23e12c93aece27c7123b64fbf3859e4ffbbb2 9f5836f54bcaf5171bd3e328d4462d0b920464f0 e8e962b9c7ceb4a6972fdadb2b39287d53cc95c5
+
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/30/
+-rw-r--r-- root/root 11012 2016-04-26 14:22 ./usr/lib/debug/.build-id/30/253512f9a4cff3a5eb697efe3b4fa35c7f6f42.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/5f/
+-rw-r--r-- root/root 20048 2016-04-26 14:22 ./usr/lib/debug/.build-id/5f/76211bbb973709cc9484f8b9c7c681dfb48a7b.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/64/
+-rw-r--r-- root/root 438276 2016-04-26 14:22 ./usr/lib/debug/.build-id/64/bda7cf8f30161939a7eb2c52903885df46351f.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/84/
+-rw-r--r-- root/root 8460 2016-04-26 14:22 ./usr/lib/debug/.build-id/84/3f27d6956db8487122181beeea46ac7abb256f.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/98/
+-rw-r--r-- root/root 19116 2016-04-26 14:22 ./usr/lib/debug/.build-id/98/d23e12c93aece27c7123b64fbf3859e4ffbbb2.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/9f/
+-rw-r--r-- root/root 11020 2016-04-26 14:22 ./usr/lib/debug/.build-id/9f/5836f54bcaf5171bd3e328d4462d0b920464f0.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/lib/debug/.build-id/e8/
+-rw-r--r-- root/root 11028 2016-04-26 14:22 ./usr/lib/debug/.build-id/e8/e962b9c7ceb4a6972fdadb2b39287d53cc95c5.debug
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 14:22 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_armel.deb
+──────────────────────────
+
+ new debian package, version 2.0.
+ size 220968 bytes: control archive=1636 bytes.
+ 808 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
+ Package: samtools
+ Version: 1.3.1-1
+ Architecture: armel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 655
+ 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 2016-04-26 14:22 ./
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/bin/
+-rwxr-xr-x root/root 17972 2016-04-26 14:22 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9768 2016-04-26 14:22 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9768 2016-04-26 14:22 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9784 2016-04-26 14:22 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5652 2016-04-26 14:22 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 383548 2016-04-26 14:22 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22136 2016-04-26 14:22 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 14:22 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 14:22 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 14:22 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 14:22 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 14:22 ./usr/share/man/man1/wgsim.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1713,20 +2201,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armel
-Build-Space: 18912
-Build-Time: 240
+Build-Space: 16452
+Build-Time: 873
Distribution: sid
-Fail-Stage: build
Host Architecture: armel
Install-Time: 35
-Job: samtools_1.3-1
-Machine Architecture: armhf
+Job: samtools_1.3.1-1
+Machine Architecture: armel
Package: samtools
-Package-Time: 349
-Source-Version: 1.3-1
-Space: 18912
-Status: attempted
-Version: 1.3-1
+Package-Time: 948
+Source-Version: 1.3.1-1
+Space: 16452
+Status: successful
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1721
-Build needed 00:05:49, 18912k disc space
+Finished at 20160426-1422
+Build needed 00:15:48, 16452k disc space
+Signature with key '08BE2BFD' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_armel.changes 08BE2BFD
+
+Successfully signed changes file
diff --git a/i386.log b/i386.log
index 66c5a52..56657cb 100644
--- a/i386.log
+++ b/i386.log
@@ -1,42 +1,47 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-grnet-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on babin.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (i386) 05 Feb 2016 16:24 ║
+║ samtools 1.3.1-1 (i386) 26 Apr 2016 12:32 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: i386
Build Architecture: i386
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-1p0oNc/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-1p0oNc' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-d81b7f8e-dedd-44c3-804b-c9cdf0fac923' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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]
+Get:1 http://mirror.1und1.de/debian unstable InRelease [196 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://mirror.1und1.de/debian unstable/main Sources [6767 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:5 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:6 http://mirror.1und1.de/debian unstable/contrib Sources [48.6 kB]
+Get:7 http://mirror.1und1.de/debian unstable/non-free Sources [84.1 kB]
+Get:8 http://mirror.1und1.de/debian unstable/main i386 Packages [7052 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main i386 Packages [137 kB]
+Get:13 http://mirror.1und1.de/debian unstable/contrib i386 Packages [51.6 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib i386 Packages [2612 B]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main i386 Packages [7052 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib i386 Packages [51.6 kB]
+Fetched 28.7 MB in 8s (3345 kB/s)
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 │
@@ -47,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 1s (3705 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 3s (1197 kB/s)
Download complete and in download only mode
Check architectures
@@ -77,16 +81,15 @@ 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-8OplFR/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-nREYoI/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-nREYoI/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -101,29 +104,28 @@ 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 18 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 29 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-8OplFR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-nREYoI/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%
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(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 ... 12366 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%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12412 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 (>= 1.3), 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-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]
+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-sLvjDt/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -137,79 +139,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 29 not upgraded.
+Need to get 26.7 MB/26.7 MB of archives.
+After this operation, 91.8 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-sLvjDt/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [994 B]
+Get:2 http://mirror.1und1.de/debian unstable/main i386 bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://mirror.1und1.de/debian unstable/main i386 groff-base i386 1.22.3-7 [1185 kB]
+Get:4 http://mirror.1und1.de/debian unstable/main i386 libbsd0 i386 0.8.3-1 [86.5 kB]
+Get:5 http://mirror.1und1.de/debian unstable/main i386 bsdmainutils i386 9.0.10 [185 kB]
+Get:6 http://mirror.1und1.de/debian unstable/main i386 libpipeline1 i386 1.4.1-2 [29.6 kB]
+Get:7 http://mirror.1und1.de/debian unstable/main i386 man-db i386 2.7.5-1 [1011 kB]
+Get:8 http://mirror.1und1.de/debian unstable/main i386 autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://mirror.1und1.de/debian unstable/main i386 libunistring0 i386 0.9.3-5.2+b1 [288 kB]
+Get:10 http://mirror.1und1.de/debian unstable/main i386 libssl1.0.2 i386 1.0.2g-2 [1718 kB]
+Get:11 http://mirror.1und1.de/debian unstable/main i386 libmagic1 i386 1:5.25-2 [261 kB]
+Get:12 http://mirror.1und1.de/debian unstable/main i386 file i386 1:5.25-2 [61.5 kB]
+Get:13 http://mirror.1und1.de/debian unstable/main i386 gettext-base i386 0.19.7-2 [116 kB]
+Get:14 http://mirror.1und1.de/debian unstable/main i386 libnettle6 i386 3.2-1 [207 kB]
+Get:15 http://mirror.1und1.de/debian unstable/main i386 libhogweed4 i386 3.2-1 [138 kB]
+Get:16 http://mirror.1und1.de/debian unstable/main i386 libidn11 i386 1.32-3 [114 kB]
+Get:17 http://mirror.1und1.de/debian unstable/main i386 libffi6 i386 3.2.1-4 [19.5 kB]
+Get:18 http://mirror.1und1.de/debian unstable/main i386 libp11-kit0 i386 0.23.2-3 [114 kB]
+Get:19 http://mirror.1und1.de/debian unstable/main i386 libtasn1-6 i386 4.8-1 [51.8 kB]
+Get:20 http://mirror.1und1.de/debian unstable/main i386 libgnutls30 i386 3.4.11-3 [812 kB]
+Get:21 http://mirror.1und1.de/debian unstable/main i386 libkeyutils1 i386 1.5.9-8 [12.5 kB]
+Get:22 http://mirror.1und1.de/debian unstable/main i386 libkrb5support0 i386 1.13.2+dfsg-5 [61.9 kB]
+Get:23 http://mirror.1und1.de/debian unstable/main i386 libk5crypto3 i386 1.13.2+dfsg-5 [116 kB]
+Get:24 http://mirror.1und1.de/debian unstable/main i386 libkrb5-3 i386 1.13.2+dfsg-5 [332 kB]
+Get:25 http://mirror.1und1.de/debian unstable/main i386 libgssapi-krb5-2 i386 1.13.2+dfsg-5 [162 kB]
+Get:26 http://mirror.1und1.de/debian unstable/main i386 libsasl2-modules-db i386 2.1.26.dfsg1-15 [67.8 kB]
+Get:27 http://mirror.1und1.de/debian unstable/main i386 libsasl2-2 i386 2.1.26.dfsg1-15 [107 kB]
+Get:28 http://mirror.1und1.de/debian unstable/main i386 libldap-2.4-2 i386 2.4.42+dfsg-2+b2 [234 kB]
+Get:29 http://mirror.1und1.de/debian unstable/main i386 libicu55 i386 55.1-7 [7762 kB]
+Get:30 http://mirror.1und1.de/debian unstable/main i386 libxml2 i386 2.9.3+dfsg1-1 [951 kB]
+Get:31 http://mirror.1und1.de/debian unstable/main i386 libsigsegv2 i386 2.10-5 [29.1 kB]
+Get:32 http://mirror.1und1.de/debian unstable/main i386 m4 i386 1.4.17-5 [255 kB]
+Get:33 http://mirror.1und1.de/debian unstable/main i386 autoconf all 2.69-10 [338 kB]
+Get:34 http://mirror.1und1.de/debian unstable/main i386 autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://mirror.1und1.de/debian unstable/main i386 automake all 1:1.15-4 [735 kB]
+Get:36 http://mirror.1und1.de/debian unstable/main i386 autopoint all 0.19.7-2 [424 kB]
+Get:37 http://mirror.1und1.de/debian unstable/main i386 libglib2.0-0 i386 2.48.0-1 [2767 kB]
+Get:38 http://mirror.1und1.de/debian unstable/main i386 libcroco3 i386 0.6.11-1 [149 kB]
+Get:39 http://mirror.1und1.de/debian unstable/main i386 gettext i386 0.19.7-2 [1481 kB]
+Get:40 http://mirror.1und1.de/debian unstable/main i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://mirror.1und1.de/debian unstable/main i386 po-debconf all 1.0.19 [249 kB]
+Get:42 http://mirror.1und1.de/debian unstable/main i386 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://mirror.1und1.de/debian unstable/main i386 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://mirror.1und1.de/debian unstable/main i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://mirror.1und1.de/debian unstable/main i386 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://mirror.1und1.de/debian unstable/main i386 libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://mirror.1und1.de/debian unstable/main i386 dh-autoreconf all 12 [15.8 kB]
+Get:48 http://mirror.1und1.de/debian unstable/main i386 debhelper all 9.20160403 [800 kB]
+Get:49 http://mirror.1und1.de/debian unstable/main i386 libnghttp2-14 i386 1.9.2-1 [81.1 kB]
+Get:50 http://mirror.1und1.de/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d-1+b1 [64.1 kB]
+Get:51 http://mirror.1und1.de/debian unstable/main i386 libssh2-1 i386 1.5.0-2.1 [140 kB]
+Get:52 http://mirror.1und1.de/debian unstable/main i386 libcurl3-gnutls i386 7.47.0-1 [296 kB]
+Get:53 http://mirror.1und1.de/debian unstable/main i386 libhts1 i386 1.3.1-1 [275 kB]
+Get:54 http://mirror.1und1.de/debian unstable/main i386 libhts-dev i386 1.3.1-1 [321 kB]
+Get:55 http://mirror.1und1.de/debian unstable/main i386 libio-pty-perl i386 1:1.08-1.1+b1 [33.8 kB]
+Get:56 http://mirror.1und1.de/debian unstable/main i386 libtinfo-dev i386 6.0+20160319-1 [76.4 kB]
+Get:57 http://mirror.1und1.de/debian unstable/main i386 libncurses5-dev i386 6.0+20160319-1 [177 kB]
+Get:58 http://mirror.1und1.de/debian unstable/main i386 tabix i386 1.3.1-1 [261 kB]
+Get:59 http://mirror.1und1.de/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 21.1 MB in 1s (11.5 MB/s)
+Fetched 26.7 MB in 2s (11.5 MB/s)
Selecting previously unselected package bash-completion.
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-Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
-Unpacking bash-completion (1:2.1-4.2) ...
+(Reading database ...
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(Reading database ... 12412 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_i386.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:i386.
+Preparing to unpack .../libbsd0_0.8.3-1_i386.deb ...
+Unpacking libbsd0:i386 (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_i386.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_i386.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:i386.
Preparing to unpack .../libpipeline1_1.4.1-2_i386.deb ...
Unpacking libpipeline1:i386 (1.4.1-2) ...
@@ -219,12 +257,12 @@ 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) ...
+Selecting previously unselected package libssl1.0.2:i386.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_i386.deb ...
+Unpacking libssl1.0.2:i386 (1.0.2g-2) ...
Selecting previously unselected package libmagic1:i386.
Preparing to unpack .../libmagic1_1%3a5.25-2_i386.deb ...
Unpacking libmagic1:i386 (1:5.25-2) ...
@@ -234,30 +272,78 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_i386.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:i386.
+Preparing to unpack .../libnettle6_3.2-1_i386.deb ...
+Unpacking libnettle6:i386 (3.2-1) ...
+Selecting previously unselected package libhogweed4:i386.
+Preparing to unpack .../libhogweed4_3.2-1_i386.deb ...
+Unpacking libhogweed4:i386 (3.2-1) ...
+Selecting previously unselected package libidn11:i386.
+Preparing to unpack .../libidn11_1.32-3_i386.deb ...
+Unpacking libidn11:i386 (1.32-3) ...
+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 libp11-kit0:i386.
+Preparing to unpack .../libp11-kit0_0.23.2-3_i386.deb ...
+Unpacking libp11-kit0:i386 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:i386.
+Preparing to unpack .../libtasn1-6_4.8-1_i386.deb ...
+Unpacking libtasn1-6:i386 (4.8-1) ...
+Selecting previously unselected package libgnutls30:i386.
+Preparing to unpack .../libgnutls30_3.4.11-3_i386.deb ...
+Unpacking libgnutls30:i386 (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:i386.
+Preparing to unpack .../libkeyutils1_1.5.9-8_i386.deb ...
+Unpacking libkeyutils1:i386 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:i386.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_i386.deb ...
+Unpacking libkrb5support0:i386 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:i386.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_i386.deb ...
+Unpacking libk5crypto3:i386 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:i386.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_i386.deb ...
+Unpacking libkrb5-3:i386 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:i386.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_i386.deb ...
+Unpacking libgssapi-krb5-2:i386 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:i386.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_i386.deb ...
+Unpacking libsasl2-modules-db:i386 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:i386.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_i386.deb ...
+Unpacking libsasl2-2:i386 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:i386.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_i386.deb ...
+Unpacking libldap-2.4-2:i386 (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:i386.
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 libsigsegv2:i386.
+Preparing to unpack .../libsigsegv2_2.10-5_i386.deb ...
+Unpacking libsigsegv2:i386 (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:i386.
-Preparing to unpack .../libglib2.0-0_2.46.2-3_i386.deb ...
-Unpacking libglib2.0-0:i386 (2.46.2-3) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.48.0-1) ...
Selecting previously unselected package libcroco3:i386.
Preparing to unpack .../libcroco3_0.6.11-1_i386.deb ...
Unpacking libcroco3:i386 (0.6.11-1) ...
@@ -271,87 +357,128 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:i386.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_i386.deb ...
+Unpacking libnghttp2-14:i386 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:i386.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_i386.deb ...
+Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:i386.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_i386.deb ...
+Unpacking libssh2-1:i386 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:i386.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_i386.deb ...
+Unpacking libcurl3-gnutls:i386 (7.47.0-1) ...
Selecting previously unselected package libhts1:i386.
-Preparing to unpack .../libhts1_1.3-1_i386.deb ...
-Unpacking libhts1:i386 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_i386.deb ...
+Unpacking libhts1:i386 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:i386.
-Preparing to unpack .../libhts-dev_1.3-1_i386.deb ...
-Unpacking libhts-dev:i386 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_i386.deb ...
+Unpacking libhts-dev:i386 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:i386.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_i386.deb ...
-Unpacking libtinfo-dev:i386 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_i386.deb ...
+Unpacking libtinfo-dev:i386 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_i386.deb ...
+Unpacking libncurses5-dev:i386 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_i386.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_i386.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:i386 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:i386 (1.0.2g-2) ...
Setting up libmagic1:i386 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:i386 (3.2-1) ...
+Setting up libhogweed4:i386 (3.2-1) ...
+Setting up libidn11:i386 (1.32-3) ...
+Setting up libffi6:i386 (3.2.1-4) ...
+Setting up libp11-kit0:i386 (0.23.2-3) ...
+Setting up libtasn1-6:i386 (4.8-1) ...
+Setting up libgnutls30:i386 (3.4.11-3) ...
+Setting up libkeyutils1:i386 (1.5.9-8) ...
+Setting up libkrb5support0:i386 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:i386 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:i386 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:i386 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:i386 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:i386 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:i386 (2.4.42+dfsg-2+b2) ...
Setting up libicu55:i386 (55.1-7) ...
Setting up libxml2:i386 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:i386 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:i386 (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:i386 (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:i386 (1.3-1) ...
-Setting up libhts-dev:i386 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:i386 (1.9.2-1) ...
+Setting up librtmp1:i386 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:i386 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:i386 (7.47.0-1) ...
+Setting up libhts1:i386 (1.3.1-1) ...
+Setting up libhts-dev:i386 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:i386 (6.0+20160319-1) ...
+Setting up libncurses5-dev:i386 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -359,8 +486,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -371,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -389,7 +516,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=4
+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
@@ -398,23 +525,23 @@ SCHROOT_CHROOT_NAME=sid-i386-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-i386-sbuild-6c935caa-c350-4653-bfac-a4bfadd6ca0a
+SCHROOT_SESSION_ID=sid-i386-sbuild-d81b7f8e-dedd-44c3-804b-c9cdf0fac923
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=2
+XDG_SESSION_ID=1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture i386
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -422,7 +549,7 @@ dh clean --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
touch config.mk
dh_auto_clean --
- make -j4 distclean
+ 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
@@ -461,15 +588,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -481,6 +608,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -499,68 +628,65 @@ 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 -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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
@@ -569,14 +695,17 @@ 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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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/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/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/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/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»'
@@ -584,40 +713,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j4 test BGZIP=/usr/bin/bgzip
+ make -j8 test VERBOSE=1 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/kLkF7CJo2N/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/uInuwt81Nj/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/kLkF7CJo2N/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/uInuwt81Nj/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/kLkF7CJo2N/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/uInuwt81Nj/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/kLkF7CJo2N/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/uInuwt81Nj/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -625,7 +754,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/kLkF7CJo2N/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/uInuwt81Nj/dict.fa.gz
.. ok
test_dict:
@@ -633,17 +762,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/kLkF7CJo2N/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/uInuwt81Nj/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/kLkF7CJo2N/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/uInuwt81Nj/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/kLkF7CJo2N/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/uInuwt81Nj/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -651,35 +780,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/kLkF7CJo2N/mpileup.bam.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/uInuwt81Nj/mpileup.bam.list -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/uInuwt81Nj/mpileup.cram.list -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/uInuwt81Nj/mpileup.bam.list -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/uInuwt81Nj/mpileup.cram.list -f /tmp/uInuwt81Nj/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/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/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/uInuwt81Nj/mpileup.cram.list -f /tmp/uInuwt81Nj/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/kLkF7CJo2N/mpileup.cram.list -f /tmp/kLkF7CJo2N/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/uInuwt81Nj/mpileup.cram.list -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:1050-1060 /tmp/uInuwt81Nj/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/uInuwt81Nj/mpileup.ref.fa.gz -r17:1050-1060 /tmp/uInuwt81Nj/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -929,41 +1058,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/uInuwt81Nj/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/uInuwt81Nj/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/uInuwt81Nj/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/uInuwt81Nj/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/uInuwt81Nj/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/uInuwt81Nj/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/kLkF7CJo2N/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/uInuwt81Nj/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/kLkF7CJo2N/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/uInuwt81Nj/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -977,419 +1106,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 74: Count -l Library 3 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 75: Filter -l Library 3 (BAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 76: Count -l Library 3 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 141: Count Z (BAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 264: Big SAM -> BAM .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 267: Big SAM -> CRAM .. ok
+ 267: Make CRAM with no UR field .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 270: Big SAM -> BAM .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 273: Big SAM -> CRAM .. ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
+
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1537,7 +1678,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/pFNRNGx9cU - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/3ffov1d8ui - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1557,15 +1698,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/uInuwt81Nj/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/uInuwt81Nj/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/kLkF7CJo2N/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/uInuwt81Nj/sorttmp
.. ok
test_fixmate:
@@ -1619,8 +1760,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1668,10 +1819,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1681,12 +1832,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1716,7 +1864,7 @@ 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 -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
@@ -1768,7 +1916,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1791,41 +1939,41 @@ 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/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
+ 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/91/698cc2f1ae4fd9001b6ee178f8d52047fbc935.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/698cc2f1ae4fd9001b6ee178f8d52047fbc935.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/698cc2f1ae4fd9001b6ee178f8d52047fbc935.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/70777fc26113a99f6855a9462f0caa2b276a8f.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/70777fc26113a99f6855a9462f0caa2b276a8f.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/09/70777fc26113a99f6855a9462f0caa2b276a8f.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/04
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/04/49e831303963075d3d9089572596fb44998308.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/04/49e831303963075d3d9089572596fb44998308.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/04/49e831303963075d3d9089572596fb44998308.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8/b2728ec8b687a773db1ea4f13f998b69b63faf.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8/b2728ec8b687a773db1ea4f13f998b69b63faf.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/f8/b2728ec8b687a773db1ea4f13f998b69b63faf.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/053304085274e5f4bcc8d40d76312072b4f5f6.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/053304085274e5f4bcc8d40d76312072b4f5f6.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8a/053304085274e5f4bcc8d40d76312072b4f5f6.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/54
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/54/a2420afae8c166260178327c7323467d1afd5b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/54/a2420afae8c166260178327c7323467d1afd5b.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/54/a2420afae8c166260178327c7323467d1afd5b.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c7
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c7/7c2985a756239fb5fa5cdeda537ac97636d104.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c7/7c2985a756239fb5fa5cdeda537ac97636d104.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/08/ded11e29249f2237075913304f8f436c6f31eb.debug debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c7/7c2985a756239fb5fa5cdeda537ac97636d104.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
@@ -1833,13 +1981,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam 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/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 -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=0449e831303963075d3d9089572596fb44998308 0970777fc26113a99f6855a9462f0caa2b276a8f 54a2420afae8c166260178327c732346 [...]
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
@@ -1858,17 +2006,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_i386.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_i386.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_i386.deb'.
- dpkg-genchanges -B -mamd64 / i386 Build Daemon (x86-grnet-01) <buildd_amd64-x86-grnet-01 at buildd.debian.org> >../samtools_1.3-1_i386.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_i386.deb'.
+ dpkg-genchanges -B -mamd64/i386 Build Daemon (babin) <buildd-babin at buildd.debian.org> >../samtools_1.3.1-1_i386.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1626
+Build finished at 20160426-1234
Finished
────────
@@ -1885,107 +2033,99 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_i386.changes:
-────────────────────────────
+samtools_1.3.1-1_i386.changes:
+──────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: i386
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-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>
+Maintainer: amd64/i386 Build Daemon (babin) <buildd-babin at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 39eb05a2533e6779f2a0e688b1bf2c675b863281 425484 samtools-dbgsym_1.3-1_i386.deb
- a5bb2525c1c8fe6db8075dda90463d0e3f1c72c1 253866 samtools_1.3-1_i386.deb
+ dcf6adf4d2477e20192785091acbc402d933a0d1 434384 samtools-dbgsym_1.3.1-1_i386.deb
+ 2d04356e2567dd6a0744ddcf3d508d75f1bbb189 258358 samtools_1.3.1-1_i386.deb
Checksums-Sha256:
- 9cff43d925cedb099518365844dbc629cf143eaf2ff0b5ad1e0dcb4b8dc3ada4 425484 samtools-dbgsym_1.3-1_i386.deb
- fc7bb592cfe63039f4f9e39138ce35d77c68172f5e02ff86ec5f2f20212a7855 253866 samtools_1.3-1_i386.deb
+ 3215a7515f6a7f958b360e3df0c62f1a9e75d93b3c15465f9729b6aec37ac628 434384 samtools-dbgsym_1.3.1-1_i386.deb
+ 2304535b3031cbf6bad111ecfec6709a29cf954bd4783b388058e5be50617fa5 258358 samtools_1.3.1-1_i386.deb
Files:
- 11722047d3a93c05cf27a36824f7ebf3 425484 debug extra samtools-dbgsym_1.3-1_i386.deb
- e2a906a2cb7feceb94193290147ec437 253866 science optional samtools_1.3-1_i386.deb
+ 65b72c454fa1cb4ed75378486593de61 434384 debug extra samtools-dbgsym_1.3.1-1_i386.deb
+ dcadd0bd100c956907e0b395dcc77bfa 258358 science optional samtools_1.3.1-1_i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_i386.deb
-──────────────────────────────
+samtools-dbgsym_1.3.1-1_i386.deb
+────────────────────────────────
new debian package, version 2.0.
- size 425484 bytes: control archive=815 bytes.
- 645 bytes, 13 lines control
+ size 434384 bytes: control archive=820 bytes.
+ 649 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 480
- Depends: samtools (= 1.3-1)
+ Installed-Size: 489
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-───────────────────────
+ Build-Ids: 0449e831303963075d3d9089572596fb44998308 0970777fc26113a99f6855a9462f0caa2b276a8f 54a2420afae8c166260178327c7323467d1afd5b 8a053304085274e5f4bcc8d40d76312072b4f5f6 91698cc2f1ae4fd9001b6ee178f8d52047fbc935 c77c2985a756239fb5fa5cdeda537ac97636d104 f8b2728ec8b687a773db1ea4f13f998b69b63faf
+
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/04/
+-rw-r--r-- root/root 9584 2016-04-26 12:34 ./usr/lib/debug/.build-id/04/49e831303963075d3d9089572596fb44998308.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/09/
+-rw-r--r-- root/root 7088 2016-04-26 12:34 ./usr/lib/debug/.build-id/09/70777fc26113a99f6855a9462f0caa2b276a8f.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/54/
+-rw-r--r-- root/root 18148 2016-04-26 12:34 ./usr/lib/debug/.build-id/54/a2420afae8c166260178327c7323467d1afd5b.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/8a/
+-rw-r--r-- root/root 9472 2016-04-26 12:34 ./usr/lib/debug/.build-id/8a/053304085274e5f4bcc8d40d76312072b4f5f6.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/91/
+-rw-r--r-- root/root 16936 2016-04-26 12:34 ./usr/lib/debug/.build-id/91/698cc2f1ae4fd9001b6ee178f8d52047fbc935.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/c7/
+-rw-r--r-- root/root 409860 2016-04-26 12:34 ./usr/lib/debug/.build-id/c7/7c2985a756239fb5fa5cdeda537ac97636d104.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/lib/debug/.build-id/f8/
+-rw-r--r-- root/root 9460 2016-04-26 12:34 ./usr/lib/debug/.build-id/f8/b2728ec8b687a773db1ea4f13f998b69b63faf.debug
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 12:34 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_i386.deb
+─────────────────────────
new debian package, version 2.0.
- size 253866 bytes: control archive=1629 bytes.
- 805 bytes, 17 lines control
+ size 258358 bytes: control archive=1629 bytes.
+ 807 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 720
+ Installed-Size: 727
Depends: libc6 (>= 2.7), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -1999,48 +2139,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/bin/
+-rwxr-xr-x root/root 17956 2016-04-26 12:34 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9748 2016-04-26 12:34 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2016-04-26 12:34 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9768 2016-04-26 12:34 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5636 2016-04-26 12:34 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 457284 2016-04-26 12:34 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22116 2016-04-26 12:34 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 12:34 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 12:34 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 12:34 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 12:34 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 12:34 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2060,23 +2200,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: i386
-Build-Space: 16388
-Build-Time: 78
+Build-Space: 16496
+Build-Time: 122
Distribution: sid
Host Architecture: i386
-Install-Time: 13
-Job: samtools_1.3-1
+Install-Time: 19
+Job: samtools_1.3.1-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 105
-Source-Version: 1.3-1
-Space: 16388
+Package-Time: 163
+Source-Version: 1.3.1-1
+Space: 16496
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160426-1234
+Build needed 00:02:43, 16496k disc space
+Signature with key 'A6BA9F19' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_i386.changes A6BA9F19
Successfully signed changes file
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index c8dddf0..e71a1e6 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 1.3-1 (kfreebsd-amd64) 05 Feb 2016 16:25 ║
+║ samtools 1.3.1-1 (kfreebsd-amd64) 26 Apr 2016 12:37 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: kfreebsd-amd64
Host Architecture: kfreebsd-amd64
Build Architecture: kfreebsd-amd64
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-7xZYKp/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-7xZYKp' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-a-sbuild-1461674226-56611' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [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)
+Get:1 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:2 http://ftp.de.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-amd64 Packages [98.9 kB]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-amd64 Packages [2296 B]
+Get:10 http://ftp.de.debian.org/debian unstable/main Sources [6767 kB]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-amd64 Packages [6465 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [39.7 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 Packages [6465 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-amd64 Packages [39.7 kB]
+Fetched 27.5 MB in 11s (2423 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 0s (6295 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (6087 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,16 @@ 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-ySPn1z/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-AIFYFq/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-AIFYFq/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-AIFYFq/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 +105,29 @@ 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 6 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 16 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-ySPn1z/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
+Get:1 file:/«BUILDDIR»/resolver-AIFYFq/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 ... 12046 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 ... 12068 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 (>= 4:5.3), 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'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-v9Y8wb/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ Packages [752 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +141,105 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl libgcrypt20
+ libglib2.0-0 libgnutls30 libgpg-error0 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libldap-2.4-2 libmagic1 libncurses5-dev
+ libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff rng-tools gnutls-bin
+ ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl libgcrypt20
+ libglib2.0-0 libgnutls30 libgpg-error0 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libldap-2.4-2 libmagic1 libncurses5-dev
+ libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 55 newly installed, 0 to remove and 16 not upgraded.
+Need to get 25.6 MB/25.6 MB of archives.
+After this operation, 88.6 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-v9Y8wb/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [996 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 bash-completion all 1:2.1-4.3 [178 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:4 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 bsdmainutils kfreebsd-amd64 9.0.10 [184 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 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:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libunistring0 kfreebsd-amd64 0.9.3-5.2+b1 [287 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libssl1.0.2 kfreebsd-amd64 1.0.2g-2 [1285 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 0.19.7-2 [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 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]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libgpg-error0 kfreebsd-amd64 1.22-1 [107 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libgcrypt20 kfreebsd-amd64 1.7.0-2 [484 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libnettle6 kfreebsd-amd64 3.2-1 [191 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhogweed4 kfreebsd-amd64 3.2-1 [136 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libidn11 kfreebsd-amd64 1.32-3 [113 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libffi6 kfreebsd-amd64 3.2.1-4 [19.8 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libp11-kit0 kfreebsd-amd64 0.23.2-3+b1 [111 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtasn1-6 kfreebsd-amd64 4.8-1 [49.5 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libgnutls30 kfreebsd-amd64 3.4.11-3 [791 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libsasl2-modules-db kfreebsd-amd64 2.1.26.dfsg1-15 [66.9 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libsasl2-2 kfreebsd-amd64 2.1.26.dfsg1-15 [104 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libldap-2.4-2 kfreebsd-amd64 2.4.42+dfsg-2+b2 [223 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libicu55 kfreebsd-amd64 55.1-7 [7648 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libxml2 kfreebsd-amd64 2.9.3+dfsg1-1 [888 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libsigsegv2 kfreebsd-amd64 2.10-5 [27.8 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 m4 kfreebsd-amd64 1.4.17-5 [255 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autoconf all 2.69-10 [338 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autotools-dev all 20150820.1 [71.7 kB]
+Get:31 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 automake all 1:1.15-4 [735 kB]
+Get:32 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 autopoint all 0.19.7-2 [424 kB]
+Get:33 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libglib2.0-0 kfreebsd-amd64 2.48.0-1 [2694 kB]
+Get:34 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libcroco3 kfreebsd-amd64 0.6.11-1 [143 kB]
+Get:35 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 gettext kfreebsd-amd64 0.19.7-2 [1475 kB]
+Get:36 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:37 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 po-debconf all 1.0.19 [249 kB]
+Get:38 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:39 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:40 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:41 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:42 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtool all 2.4.6-0.1 [200 kB]
+Get:43 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 dh-autoreconf all 12 [15.8 kB]
+Get:44 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 debhelper all 9.20160403 [800 kB]
+Get:45 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libnghttp2-14 kfreebsd-amd64 1.9.2-1 [76.3 kB]
+Get:46 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 librtmp1 kfreebsd-amd64 2.4+20151223.gitfa8646d-1+b1 [60.1 kB]
+Get:47 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libssh2-1 kfreebsd-amd64 1.5.0-2.1 [133 kB]
+Get:48 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libcurl3-gnutls kfreebsd-amd64 7.47.0-1 [273 kB]
+Get:49 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts1 kfreebsd-amd64 1.3.1-1 [257 kB]
+Get:50 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libhts-dev kfreebsd-amd64 1.3.1-1 [315 kB]
+Get:51 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:52 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libtinfo-dev kfreebsd-amd64 6.0+20160319-1 [77.4 kB]
+Get:53 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 libncurses5-dev kfreebsd-amd64 6.0+20160319-1 [173 kB]
+Get:54 http://ftp.de.debian.org/debian unstable/main kfreebsd-amd64 tabix kfreebsd-amd64 1.3.1-1 [252 kB]
+Get:55 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 20.6 MB in 2s (9300 kB/s)
+Fetched 25.6 MB in 2s (9117 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
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(Reading database ... 12068 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
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) ...
+Preparing to unpack .../bsdmainutils_9.0.10_kfreebsd-amd64.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:kfreebsd-amd64.
Preparing to unpack .../libpipeline1_1.4.1-2_kfreebsd-amd64.deb ...
Unpacking libpipeline1:kfreebsd-amd64 (1.4.1-2) ...
@@ -224,12 +249,12 @@ 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: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) ...
+Selecting previously unselected package libssl1.0.2:kfreebsd-amd64.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_kfreebsd-amd64.deb ...
+Unpacking libssl1.0.2:kfreebsd-amd64 (1.0.2g-2) ...
Selecting previously unselected package libmagic1:kfreebsd-amd64.
Preparing to unpack .../libmagic1_1%3a5.25-2_kfreebsd-amd64.deb ...
Unpacking libmagic1:kfreebsd-amd64 (1:5.25-2) ...
@@ -239,30 +264,69 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_kfreebsd-amd64.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libgpg-error0:kfreebsd-amd64.
+Preparing to unpack .../libgpg-error0_1.22-1_kfreebsd-amd64.deb ...
+Unpacking libgpg-error0:kfreebsd-amd64 (1.22-1) ...
+Selecting previously unselected package libgcrypt20:kfreebsd-amd64.
+Preparing to unpack .../libgcrypt20_1.7.0-2_kfreebsd-amd64.deb ...
+Unpacking libgcrypt20:kfreebsd-amd64 (1.7.0-2) ...
+Selecting previously unselected package libnettle6:kfreebsd-amd64.
+Preparing to unpack .../libnettle6_3.2-1_kfreebsd-amd64.deb ...
+Unpacking libnettle6:kfreebsd-amd64 (3.2-1) ...
+Selecting previously unselected package libhogweed4:kfreebsd-amd64.
+Preparing to unpack .../libhogweed4_3.2-1_kfreebsd-amd64.deb ...
+Unpacking libhogweed4:kfreebsd-amd64 (3.2-1) ...
+Selecting previously unselected package libidn11:kfreebsd-amd64.
+Preparing to unpack .../libidn11_1.32-3_kfreebsd-amd64.deb ...
+Unpacking libidn11:kfreebsd-amd64 (1.32-3) ...
+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 libp11-kit0:kfreebsd-amd64.
+Preparing to unpack .../libp11-kit0_0.23.2-3+b1_kfreebsd-amd64.deb ...
+Unpacking libp11-kit0:kfreebsd-amd64 (0.23.2-3+b1) ...
+Selecting previously unselected package libtasn1-6:kfreebsd-amd64.
+Preparing to unpack .../libtasn1-6_4.8-1_kfreebsd-amd64.deb ...
+Unpacking libtasn1-6:kfreebsd-amd64 (4.8-1) ...
+Selecting previously unselected package libgnutls30:kfreebsd-amd64.
+Preparing to unpack .../libgnutls30_3.4.11-3_kfreebsd-amd64.deb ...
+Unpacking libgnutls30:kfreebsd-amd64 (3.4.11-3) ...
+Selecting previously unselected package libsasl2-modules-db:kfreebsd-amd64.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_kfreebsd-amd64.deb ...
+Unpacking libsasl2-modules-db:kfreebsd-amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:kfreebsd-amd64.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_kfreebsd-amd64.deb ...
+Unpacking libsasl2-2:kfreebsd-amd64 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:kfreebsd-amd64.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_kfreebsd-amd64.deb ...
+Unpacking libldap-2.4-2:kfreebsd-amd64 (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:kfreebsd-amd64.
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 libsigsegv2:kfreebsd-amd64.
+Preparing to unpack .../libsigsegv2_2.10-5_kfreebsd-amd64.deb ...
+Unpacking libsigsegv2:kfreebsd-amd64 (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_kfreebsd-amd64.deb ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (2.48.0-1) ...
Selecting previously unselected package libcroco3:kfreebsd-amd64.
Preparing to unpack .../libcroco3_0.6.11-1_kfreebsd-amd64.deb ...
Unpacking libcroco3:kfreebsd-amd64 (0.6.11-1) ...
@@ -276,87 +340,124 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:kfreebsd-amd64.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_kfreebsd-amd64.deb ...
+Unpacking libnghttp2-14:kfreebsd-amd64 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:kfreebsd-amd64.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_kfreebsd-amd64.deb ...
+Unpacking librtmp1:kfreebsd-amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:kfreebsd-amd64.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_kfreebsd-amd64.deb ...
+Unpacking libssh2-1:kfreebsd-amd64 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:kfreebsd-amd64.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_kfreebsd-amd64.deb ...
+Unpacking libcurl3-gnutls:kfreebsd-amd64 (7.47.0-1) ...
Selecting previously unselected package libhts1:kfreebsd-amd64.
-Preparing to unpack .../libhts1_1.3-1_kfreebsd-amd64.deb ...
-Unpacking libhts1:kfreebsd-amd64 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts1:kfreebsd-amd64 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:kfreebsd-amd64.
-Preparing to unpack .../libhts-dev_1.3-1_kfreebsd-amd64.deb ...
-Unpacking libhts-dev:kfreebsd-amd64 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts-dev:kfreebsd-amd64 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_kfreebsd-amd64.deb ...
-Unpacking libtinfo-dev:kfreebsd-amd64 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_kfreebsd-amd64.deb ...
+Unpacking libtinfo-dev:kfreebsd-amd64 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_kfreebsd-amd64.deb ...
+Unpacking libncurses5-dev:kfreebsd-amd64 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.3-1_kfreebsd-amd64.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_kfreebsd-amd64.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-6) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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:kfreebsd-amd64 (2.10-4+b1) ...
Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
+Setting up libssl1.0.2:kfreebsd-amd64 (1.0.2g-2) ...
Setting up libmagic1:kfreebsd-amd64 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libgpg-error0:kfreebsd-amd64 (1.22-1) ...
+Setting up libgcrypt20:kfreebsd-amd64 (1.7.0-2) ...
+Setting up libnettle6:kfreebsd-amd64 (3.2-1) ...
+Setting up libhogweed4:kfreebsd-amd64 (3.2-1) ...
+Setting up libidn11:kfreebsd-amd64 (1.32-3) ...
+Setting up libffi6:kfreebsd-amd64 (3.2.1-4) ...
+Setting up libp11-kit0:kfreebsd-amd64 (0.23.2-3+b1) ...
+Setting up libtasn1-6:kfreebsd-amd64 (4.8-1) ...
+Setting up libgnutls30:kfreebsd-amd64 (3.4.11-3) ...
+Setting up libsasl2-modules-db:kfreebsd-amd64 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:kfreebsd-amd64 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:kfreebsd-amd64 (2.4.42+dfsg-2+b2) ...
Setting up libicu55:kfreebsd-amd64 (55.1-7) ...
Setting up libxml2:kfreebsd-amd64 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:kfreebsd-amd64 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-amd64 (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:kfreebsd-amd64 (1.3-1) ...
-Setting up libhts-dev:kfreebsd-amd64 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:kfreebsd-amd64 (1.9.2-1) ...
+Setting up librtmp1:kfreebsd-amd64 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:kfreebsd-amd64 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:kfreebsd-amd64 (7.47.0-1) ...
+Setting up libhts1:kfreebsd-amd64 (1.3.1-1) ...
+Setting up libhts-dev:kfreebsd-amd64 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:kfreebsd-amd64 (6.0+20160319-1) ...
+Setting up libncurses5-dev:kfreebsd-amd64 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-6) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -364,8 +465,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.22-6 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +477,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -403,7 +504,7 @@ SCHROOT_CHROOT_NAME=sid-k-a-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-k-a-sbuild-1454689512-17467
+SCHROOT_SESSION_ID=sid-k-a-sbuild-1461674226-56611
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -413,11 +514,11 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture kfreebsd-amd64
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -464,15 +565,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -484,6 +585,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,66 +607,66 @@ dh_auto_build -- \
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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
@@ -587,40 +690,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j2 test BGZIP=/usr/bin/bgzip
+ make -j2 test VERBOSE=1 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/9n3LVwBXro/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/XwfOK3bSzj/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/9n3LVwBXro/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/XwfOK3bSzj/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/9n3LVwBXro/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/XwfOK3bSzj/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/9n3LVwBXro/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/XwfOK3bSzj/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -628,7 +731,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/9n3LVwBXro/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/XwfOK3bSzj/dict.fa.gz
.. ok
test_dict:
@@ -636,17 +739,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/9n3LVwBXro/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/XwfOK3bSzj/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/9n3LVwBXro/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/XwfOK3bSzj/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/9n3LVwBXro/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/XwfOK3bSzj/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -654,35 +757,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/9n3LVwBXro/mpileup.bam.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/XwfOK3bSzj/mpileup.bam.list -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/XwfOK3bSzj/mpileup.cram.list -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/XwfOK3bSzj/mpileup.bam.list -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/XwfOK3bSzj/mpileup.cram.list -f /tmp/XwfOK3bSzj/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/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/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/XwfOK3bSzj/mpileup.cram.list -f /tmp/XwfOK3bSzj/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/9n3LVwBXro/mpileup.cram.list -f /tmp/9n3LVwBXro/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/XwfOK3bSzj/mpileup.cram.list -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XwfOK3bSzj/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/XwfOK3bSzj/mpileup.ref.fa.gz -r17:1050-1060 /tmp/XwfOK3bSzj/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -932,41 +1035,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/9n3LVwBXro/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/XwfOK3bSzj/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/9n3LVwBXro/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/XwfOK3bSzj/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/9n3LVwBXro/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/XwfOK3bSzj/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/9n3LVwBXro/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/XwfOK3bSzj/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/XwfOK3bSzj/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/XwfOK3bSzj/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/9n3LVwBXro/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/XwfOK3bSzj/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/9n3LVwBXro/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/XwfOK3bSzj/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -980,419 +1083,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 141: Count Z (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 142: Region Z (CRAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 267: Make CRAM with no UR field .. ok
- 264: Big SAM -> BAM .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 270: Big SAM -> BAM .. ok
- 267: Big SAM -> CRAM .. ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 273: Big SAM -> CRAM .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 280: Subsample 0.5 (BAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 281: Subsample 0.8 (BAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1540,7 +1655,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/jHQjuAIqo4 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/3sAIYyd0GO - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1560,15 +1675,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/XwfOK3bSzj/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/XwfOK3bSzj/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/9n3LVwBXro/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/XwfOK3bSzj/sorttmp
.. ok
test_fixmate:
@@ -1622,8 +1737,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1671,10 +1796,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1684,12 +1809,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1771,7 +1893,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1794,41 +1916,41 @@ 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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/ea149388acdd37dcc276ea5a4c78eca3fdea9d.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/ea149388acdd37dcc276ea5a4c78eca3fdea9d.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e9/ea149388acdd37dcc276ea5a4c78eca3fdea9d.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/7bb632d8ca955be06f23f51430e5d50b1bdfef.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/7bb632d8ca955be06f23f51430e5d50b1bdfef.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/30/7bb632d8ca955be06f23f51430e5d50b1bdfef.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/59f4aecfcd3c11f39d0334e3f926410dead811.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/59f4aecfcd3c11f39d0334e3f926410dead811.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/14/59f4aecfcd3c11f39d0334e3f926410dead811.debug debian/samtools/usr/bin/maq2sam-long
+ 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-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/2231ddcf678724467b5dcad497fc2393e7d619.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/2231ddcf678724467b5dcad497fc2393e7d619.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8d/2231ddcf678724467b5dcad497fc2393e7d619.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/a423279fc2e61a58cc44d813e66529f7111f30.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/a423279fc2e61a58cc44d813e66529f7111f30.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/91/a423279fc2e61a58cc44d813e66529f7111f30.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/584b59f5ff63a28c4d5fc2106762b21dcb62d9.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/584b59f5ff63a28c4d5fc2106762b21dcb62d9.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/584b59f5ff63a28c4d5fc2106762b21dcb62d9.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/10
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/10/fafb297530608fc119c18ba3550ed9105b9ad7.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/10/fafb297530608fc119c18ba3550ed9105b9ad7.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/a5/ffb4328e7791d91606a2eb1c8fe2834de9f8e0.debug debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/10/fafb297530608fc119c18ba3550ed9105b9ad7.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
@@ -1836,13 +1958,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam 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/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 -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=10fafb297530608fc119c18ba3550ed9105b9ad7 1459f4aecfcd3c11f39d0334e3f926410dead811 307bb632d8ca955be06f23f51430e5d5 [...]
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
@@ -1861,17 +1983,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_kfreebsd-amd64.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_kfreebsd-amd64.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org> >../samtools_1.3-1_kfreebsd-amd64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org> >../samtools_1.3.1-1_kfreebsd-amd64.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1627
+Build finished at 20160426-1239
Finished
────────
@@ -1888,108 +2010,100 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_kfreebsd-amd64.changes:
-──────────────────────────────────────
+samtools_1.3.1-1_kfreebsd-amd64.changes:
+────────────────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-amd64
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-amd64 Build Daemon (fayrfax) <buildd_kfreebsd-amd64-fayrfax at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 030b9b39ccbb56882439cd2a7e3588c7ef228567 467494 samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
- 410d3edf1469334f8f73379745d702bcd465050c 246338 samtools_1.3-1_kfreebsd-amd64.deb
+ a9e07bf2cd424e25bfe54bacb7fc227afac7a876 476248 samtools-dbgsym_1.3.1-1_kfreebsd-amd64.deb
+ d5ab22e4e8cb3f2b27b75be4ec967efdf12be351 250904 samtools_1.3.1-1_kfreebsd-amd64.deb
Checksums-Sha256:
- db209a46c20bb0a891c13e08992b902314c59dfe316f6a1b6fff13c3a528bd7c 467494 samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
- 0d354dca18a2f907511417df8b26c24c1ed2e9a25605e300b86d946c4feff025 246338 samtools_1.3-1_kfreebsd-amd64.deb
+ db8736cbd0613dc0dac060d409d70040f57d9b0a1206fe5296601fa1a043c65b 476248 samtools-dbgsym_1.3.1-1_kfreebsd-amd64.deb
+ 6939d71495520c98519d94758677fdf50342a2f8c3fe771add9948597aa23428 250904 samtools_1.3.1-1_kfreebsd-amd64.deb
Files:
- efa5fa6a7d396c1fa136506bf0457dbe 467494 debug extra samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
- 63568b84eb45bf598522db79167b664b 246338 science optional samtools_1.3-1_kfreebsd-amd64.deb
+ ebcb6957604e4aa46fe565e8338c6142 476248 debug extra samtools-dbgsym_1.3.1-1_kfreebsd-amd64.deb
+ fb63378ccb424cd16d6a01bbcc903702 250904 science optional samtools_1.3.1-1_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_kfreebsd-amd64.deb
-────────────────────────────────────────
+samtools-dbgsym_1.3.1-1_kfreebsd-amd64.deb
+──────────────────────────────────────────
new debian package, version 2.0.
- size 467494 bytes: control archive=817 bytes.
- 655 bytes, 13 lines control
+ size 476248 bytes: control archive=823 bytes.
+ 659 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 539
- Depends: samtools (= 1.3-1)
+ Installed-Size: 548
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-─────────────────────────────────
+ Build-Ids: 10fafb297530608fc119c18ba3550ed9105b9ad7 1459f4aecfcd3c11f39d0334e3f926410dead811 307bb632d8ca955be06f23f51430e5d50b1bdfef 8d2231ddcf678724467b5dcad497fc2393e7d619 91a423279fc2e61a58cc44d813e66529f7111f30 b8584b59f5ff63a28c4d5fc2106762b21dcb62d9 e9ea149388acdd37dcc276ea5a4c78eca3fdea9d
+
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/10/
+-rw-r--r-- root/root 19872 2016-04-26 12:39 ./usr/lib/debug/.build-id/10/fafb297530608fc119c18ba3550ed9105b9ad7.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/14/
+-rw-r--r-- root/root 11824 2016-04-26 12:39 ./usr/lib/debug/.build-id/14/59f4aecfcd3c11f39d0334e3f926410dead811.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/30/
+-rw-r--r-- root/root 20760 2016-04-26 12:39 ./usr/lib/debug/.build-id/30/7bb632d8ca955be06f23f51430e5d50b1bdfef.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/8d/
+-rw-r--r-- root/root 11824 2016-04-26 12:39 ./usr/lib/debug/.build-id/8d/2231ddcf678724467b5dcad497fc2393e7d619.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/91/
+-rw-r--r-- root/root 11824 2016-04-26 12:39 ./usr/lib/debug/.build-id/91/a423279fc2e61a58cc44d813e66529f7111f30.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/b8/
+-rw-r--r-- root/root 9136 2016-04-26 12:39 ./usr/lib/debug/.build-id/b8/584b59f5ff63a28c4d5fc2106762b21dcb62d9.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/lib/debug/.build-id/e9/
+-rw-r--r-- root/root 455904 2016-04-26 12:39 ./usr/lib/debug/.build-id/e9/ea149388acdd37dcc276ea5a4c78eca3fdea9d.debug
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2016-04-26 12:39 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_kfreebsd-amd64.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 246338 bytes: control archive=1646 bytes.
+ size 250904 bytes: control archive=1643 bytes.
821 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 704
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 715
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2002,48 +2116,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/bin/
+-rwxr-xr-x root/root 22856 2016-04-26 12:39 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10536 2016-04-26 12:39 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10536 2016-04-26 12:39 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10576 2016-04-26 12:39 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10504 2016-04-26 12:39 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 430368 2016-04-26 12:39 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22944 2016-04-26 12:39 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 12:39 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 12:39 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 12:39 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 12:39 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 12:39 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2063,23 +2177,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-amd64
-Build-Space: 17552
-Build-Time: 91
+Build-Space: 17704
+Build-Time: 94
Distribution: sid
Host Architecture: kfreebsd-amd64
-Install-Time: 14
-Job: samtools_1.3-1
+Install-Time: 15
+Job: samtools_1.3.1-1
Machine Architecture: kfreebsd-amd64
Package: samtools
-Package-Time: 133
-Source-Version: 1.3-1
-Space: 17552
+Package-Time: 135
+Source-Version: 1.3.1-1
+Space: 17704
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1627
-Build needed 00:02:13, 17552k disc space
+Finished at 20160426-1239
+Build needed 00:02:15, 17704k disc space
Signature with key '214E2A08' requested:
- signfile /home/buildd/build/samtools_1.3-1_kfreebsd-amd64.changes 214E2A08
+ signfile /home/buildd/build/samtools_1.3.1-1_kfreebsd-amd64.changes 214E2A08
Successfully signed changes file
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index 668ca87..d316a75 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 1.3-1 (kfreebsd-i386) 05 Feb 2016 16:22 ║
+║ samtools 1.3.1-1 (kfreebsd-i386) 26 Apr 2016 12:33 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: kfreebsd-i386
Host Architecture: kfreebsd-i386
Build Architecture: kfreebsd-i386
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-AM2_km/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-AM2_km' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-k-i-sbuild-1461673981-68225' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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 [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)
+Get:1 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:2 http://ftp.de.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main Sources [6767 kB]
+Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:9 http://incoming.debian.org/debian-buildd buildd-unstable/main kfreebsd-i386 Packages [83.0 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib kfreebsd-i386 Packages [2292 B]
+Get:11 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:12 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:13 http://ftp.debian.org/debian unstable/main kfreebsd-i386 Packages [6453 kB]
+Get:14 http://ftp.debian.org/debian unstable/contrib kfreebsd-i386 Packages [39.8 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 Packages [6453 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib kfreebsd-i386 Packages [39.8 kB]
+Fetched 27.4 MB in 8s (3426 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 0s (6932 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (5931 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,16 @@ 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-w6zXKN/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-mvhxpx/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-mvhxpx/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-mvhxpx/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 +105,29 @@ 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 6 not upgraded.
-Need to get 0 B/778 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 10 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-w6zXKN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [778 B]
+Get:1 file:/«BUILDDIR»/resolver-mvhxpx/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 ... 11687 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 ... 11716 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 (>= 4:5.3), 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'.
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-WZ3xih/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Sources [485 B]
+Get:5 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ Packages [749 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +141,105 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl libgcrypt20
+ libglib2.0-0 libgnutls30 libgpg-error0 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libldap-2.4-2 libmagic1 libncurses5-dev
+ libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff rng-tools gnutls-bin
+ ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
+ libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl libgcrypt20
+ libglib2.0-0 libgnutls30 libgpg-error0 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libldap-2.4-2 libmagic1 libncurses5-dev
+ libnettle6 libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 55 newly installed, 0 to remove and 10 not upgraded.
+Need to get 25.8 MB/25.8 MB of archives.
+After this operation, 88.5 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-WZ3xih/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [998 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 bash-completion all 1:2.1-4.3 [178 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:4 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 bsdmainutils kfreebsd-i386 9.0.10 [184 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 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:8 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libunistring0 kfreebsd-i386 0.9.3-5.2+b1 [285 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libssl1.0.2 kfreebsd-i386 1.0.2g-2 [1114 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 0.19.7-2 [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 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]
+Get:13 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgpg-error0 kfreebsd-i386 1.22-1 [110 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgcrypt20 kfreebsd-i386 1.7.0-2 [458 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libnettle6 kfreebsd-i386 3.2-1 [207 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhogweed4 kfreebsd-i386 3.2-1 [138 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libidn11 kfreebsd-i386 1.32-3 [115 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libffi6 kfreebsd-i386 3.2.1-4 [18.8 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libp11-kit0 kfreebsd-i386 0.23.2-3+b1 [115 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtasn1-6 kfreebsd-i386 4.8-1 [52.0 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libgnutls30 kfreebsd-i386 3.4.11-3 [813 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsasl2-modules-db kfreebsd-i386 2.1.26.dfsg1-15 [67.8 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsasl2-2 kfreebsd-i386 2.1.26.dfsg1-15 [107 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libldap-2.4-2 kfreebsd-i386 2.4.42+dfsg-2+b2 [234 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libicu55 kfreebsd-i386 55.1-7 [7757 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libxml2 kfreebsd-i386 2.9.3+dfsg1-1 [923 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libsigsegv2 kfreebsd-i386 2.10-5 [27.9 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 m4 kfreebsd-i386 1.4.17-5 [255 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autoconf all 2.69-10 [338 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autotools-dev all 20150820.1 [71.7 kB]
+Get:31 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 automake all 1:1.15-4 [735 kB]
+Get:32 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 autopoint all 0.19.7-2 [424 kB]
+Get:33 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libglib2.0-0 kfreebsd-i386 2.48.0-1 [2760 kB]
+Get:34 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcroco3 kfreebsd-i386 0.6.11-1 [149 kB]
+Get:35 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 gettext kfreebsd-i386 0.19.7-2 [1480 kB]
+Get:36 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:37 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 po-debconf all 1.0.19 [249 kB]
+Get:38 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:39 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:40 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:41 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:42 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtool all 2.4.6-0.1 [200 kB]
+Get:43 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 dh-autoreconf all 12 [15.8 kB]
+Get:44 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 debhelper all 9.20160403 [800 kB]
+Get:45 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libnghttp2-14 kfreebsd-i386 1.9.2-1 [81.2 kB]
+Get:46 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 librtmp1 kfreebsd-i386 2.4+20151223.gitfa8646d-1+b1 [64.1 kB]
+Get:47 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libssh2-1 kfreebsd-i386 1.5.0-2.1 [140 kB]
+Get:48 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libcurl3-gnutls kfreebsd-i386 7.47.0-1 [296 kB]
+Get:49 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts1 kfreebsd-i386 1.3.1-1 [275 kB]
+Get:50 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libhts-dev kfreebsd-i386 1.3.1-1 [321 kB]
+Get:51 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:52 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libtinfo-dev kfreebsd-i386 6.0+20160319-1 [76.2 kB]
+Get:53 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 libncurses5-dev kfreebsd-i386 6.0+20160319-1 [176 kB]
+Get:54 http://ftp.de.debian.org/debian unstable/main kfreebsd-i386 tabix kfreebsd-i386 1.3.1-1 [261 kB]
+Get:55 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 20.9 MB in 1s (12.6 MB/s)
+Fetched 25.8 MB in 1s (14.1 MB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
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(Reading database ... 11716 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
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) ...
+Preparing to unpack .../bsdmainutils_9.0.10_kfreebsd-i386.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:kfreebsd-i386.
Preparing to unpack .../libpipeline1_1.4.1-2_kfreebsd-i386.deb ...
Unpacking libpipeline1:kfreebsd-i386 (1.4.1-2) ...
@@ -224,12 +249,12 @@ 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: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) ...
+Selecting previously unselected package libssl1.0.2:kfreebsd-i386.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_kfreebsd-i386.deb ...
+Unpacking libssl1.0.2:kfreebsd-i386 (1.0.2g-2) ...
Selecting previously unselected package libmagic1:kfreebsd-i386.
Preparing to unpack .../libmagic1_1%3a5.25-2_kfreebsd-i386.deb ...
Unpacking libmagic1:kfreebsd-i386 (1:5.25-2) ...
@@ -239,30 +264,69 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_kfreebsd-i386.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libgpg-error0:kfreebsd-i386.
+Preparing to unpack .../libgpg-error0_1.22-1_kfreebsd-i386.deb ...
+Unpacking libgpg-error0:kfreebsd-i386 (1.22-1) ...
+Selecting previously unselected package libgcrypt20:kfreebsd-i386.
+Preparing to unpack .../libgcrypt20_1.7.0-2_kfreebsd-i386.deb ...
+Unpacking libgcrypt20:kfreebsd-i386 (1.7.0-2) ...
+Selecting previously unselected package libnettle6:kfreebsd-i386.
+Preparing to unpack .../libnettle6_3.2-1_kfreebsd-i386.deb ...
+Unpacking libnettle6:kfreebsd-i386 (3.2-1) ...
+Selecting previously unselected package libhogweed4:kfreebsd-i386.
+Preparing to unpack .../libhogweed4_3.2-1_kfreebsd-i386.deb ...
+Unpacking libhogweed4:kfreebsd-i386 (3.2-1) ...
+Selecting previously unselected package libidn11:kfreebsd-i386.
+Preparing to unpack .../libidn11_1.32-3_kfreebsd-i386.deb ...
+Unpacking libidn11:kfreebsd-i386 (1.32-3) ...
+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 libp11-kit0:kfreebsd-i386.
+Preparing to unpack .../libp11-kit0_0.23.2-3+b1_kfreebsd-i386.deb ...
+Unpacking libp11-kit0:kfreebsd-i386 (0.23.2-3+b1) ...
+Selecting previously unselected package libtasn1-6:kfreebsd-i386.
+Preparing to unpack .../libtasn1-6_4.8-1_kfreebsd-i386.deb ...
+Unpacking libtasn1-6:kfreebsd-i386 (4.8-1) ...
+Selecting previously unselected package libgnutls30:kfreebsd-i386.
+Preparing to unpack .../libgnutls30_3.4.11-3_kfreebsd-i386.deb ...
+Unpacking libgnutls30:kfreebsd-i386 (3.4.11-3) ...
+Selecting previously unselected package libsasl2-modules-db:kfreebsd-i386.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_kfreebsd-i386.deb ...
+Unpacking libsasl2-modules-db:kfreebsd-i386 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:kfreebsd-i386.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_kfreebsd-i386.deb ...
+Unpacking libsasl2-2:kfreebsd-i386 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:kfreebsd-i386.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_kfreebsd-i386.deb ...
+Unpacking libldap-2.4-2:kfreebsd-i386 (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:kfreebsd-i386.
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 libsigsegv2:kfreebsd-i386.
+Preparing to unpack .../libsigsegv2_2.10-5_kfreebsd-i386.deb ...
+Unpacking libsigsegv2:kfreebsd-i386 (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
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) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_kfreebsd-i386.deb ...
+Unpacking libglib2.0-0:kfreebsd-i386 (2.48.0-1) ...
Selecting previously unselected package libcroco3:kfreebsd-i386.
Preparing to unpack .../libcroco3_0.6.11-1_kfreebsd-i386.deb ...
Unpacking libcroco3:kfreebsd-i386 (0.6.11-1) ...
@@ -276,87 +340,124 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:kfreebsd-i386.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_kfreebsd-i386.deb ...
+Unpacking libnghttp2-14:kfreebsd-i386 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:kfreebsd-i386.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_kfreebsd-i386.deb ...
+Unpacking librtmp1:kfreebsd-i386 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:kfreebsd-i386.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_kfreebsd-i386.deb ...
+Unpacking libssh2-1:kfreebsd-i386 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:kfreebsd-i386.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_kfreebsd-i386.deb ...
+Unpacking libcurl3-gnutls:kfreebsd-i386 (7.47.0-1) ...
Selecting previously unselected package libhts1:kfreebsd-i386.
-Preparing to unpack .../libhts1_1.3-1_kfreebsd-i386.deb ...
-Unpacking libhts1:kfreebsd-i386 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_kfreebsd-i386.deb ...
+Unpacking libhts1:kfreebsd-i386 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:kfreebsd-i386.
-Preparing to unpack .../libhts-dev_1.3-1_kfreebsd-i386.deb ...
-Unpacking libhts-dev:kfreebsd-i386 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_kfreebsd-i386.deb ...
-Unpacking libtinfo-dev:kfreebsd-i386 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_kfreebsd-i386.deb ...
+Unpacking libtinfo-dev:kfreebsd-i386 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_kfreebsd-i386.deb ...
+Unpacking libncurses5-dev:kfreebsd-i386 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.3-1_kfreebsd-i386.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_kfreebsd-i386.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-6) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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:kfreebsd-i386 (2.10-4+b1) ...
Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
+Setting up libssl1.0.2:kfreebsd-i386 (1.0.2g-2) ...
Setting up libmagic1:kfreebsd-i386 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libgpg-error0:kfreebsd-i386 (1.22-1) ...
+Setting up libgcrypt20:kfreebsd-i386 (1.7.0-2) ...
+Setting up libnettle6:kfreebsd-i386 (3.2-1) ...
+Setting up libhogweed4:kfreebsd-i386 (3.2-1) ...
+Setting up libidn11:kfreebsd-i386 (1.32-3) ...
+Setting up libffi6:kfreebsd-i386 (3.2.1-4) ...
+Setting up libp11-kit0:kfreebsd-i386 (0.23.2-3+b1) ...
+Setting up libtasn1-6:kfreebsd-i386 (4.8-1) ...
+Setting up libgnutls30:kfreebsd-i386 (3.4.11-3) ...
+Setting up libsasl2-modules-db:kfreebsd-i386 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:kfreebsd-i386 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:kfreebsd-i386 (2.4.42+dfsg-2+b2) ...
Setting up libicu55:kfreebsd-i386 (55.1-7) ...
Setting up libxml2:kfreebsd-i386 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:kfreebsd-i386 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:kfreebsd-i386 (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:kfreebsd-i386 (1.3-1) ...
-Setting up libhts-dev:kfreebsd-i386 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:kfreebsd-i386 (1.9.2-1) ...
+Setting up librtmp1:kfreebsd-i386 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:kfreebsd-i386 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:kfreebsd-i386 (7.47.0-1) ...
+Setting up libhts1:kfreebsd-i386 (1.3.1-1) ...
+Setting up libhts-dev:kfreebsd-i386 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:kfreebsd-i386 (6.0+20160319-1) ...
+Setting up libncurses5-dev:kfreebsd-i386 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-6) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -364,8 +465,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 kfreebsd-kernel-headers_10.1~8 libc0.1-dev_2.22-6 libstdc++-5-dev_5.3.1-15 libstdc++6_6.0.1-2
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +477,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -403,7 +504,7 @@ SCHROOT_CHROOT_NAME=sid-k-i-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-k-i-sbuild-1454689362-28265
+SCHROOT_SESSION_ID=sid-k-i-sbuild-1461673981-68225
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -413,11 +514,11 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture kfreebsd-i386
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -464,15 +565,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -484,6 +585,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,66 +607,66 @@ dh_auto_build -- \
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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
@@ -587,40 +690,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j2 test BGZIP=/usr/bin/bgzip
+ make -j2 test VERBOSE=1 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/lPPNrK5b5B/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/oxOkcpsI9z/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/lPPNrK5b5B/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/oxOkcpsI9z/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/lPPNrK5b5B/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/oxOkcpsI9z/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/lPPNrK5b5B/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/oxOkcpsI9z/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -628,7 +731,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/lPPNrK5b5B/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/oxOkcpsI9z/dict.fa.gz
.. ok
test_dict:
@@ -636,17 +739,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/lPPNrK5b5B/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/oxOkcpsI9z/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/lPPNrK5b5B/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/oxOkcpsI9z/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/lPPNrK5b5B/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/oxOkcpsI9z/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -654,35 +757,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/lPPNrK5b5B/mpileup.bam.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/oxOkcpsI9z/mpileup.bam.list -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/oxOkcpsI9z/mpileup.cram.list -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/oxOkcpsI9z/mpileup.bam.list -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/oxOkcpsI9z/mpileup.cram.list -f /tmp/oxOkcpsI9z/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/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/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/oxOkcpsI9z/mpileup.cram.list -f /tmp/oxOkcpsI9z/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/lPPNrK5b5B/mpileup.cram.list -f /tmp/lPPNrK5b5B/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/oxOkcpsI9z/mpileup.cram.list -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oxOkcpsI9z/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/oxOkcpsI9z/mpileup.ref.fa.gz -r17:1050-1060 /tmp/oxOkcpsI9z/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -932,41 +1035,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/oxOkcpsI9z/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/oxOkcpsI9z/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/oxOkcpsI9z/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/oxOkcpsI9z/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/oxOkcpsI9z/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/oxOkcpsI9z/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/lPPNrK5b5B/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/oxOkcpsI9z/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/lPPNrK5b5B/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/oxOkcpsI9z/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -980,419 +1083,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 141: Count Z (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 142: Region Z (CRAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 267: Make CRAM with no UR field .. ok
- 264: Big SAM -> BAM .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 270: Big SAM -> BAM .. ok
- 267: Big SAM -> CRAM .. ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 273: Big SAM -> CRAM .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 280: Subsample 0.5 (BAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 281: Subsample 0.8 (BAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1540,7 +1655,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/COjVupKv2E - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/ABhECdONHc - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1560,15 +1675,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/oxOkcpsI9z/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/oxOkcpsI9z/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/lPPNrK5b5B/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/oxOkcpsI9z/sorttmp
.. ok
test_fixmate:
@@ -1622,8 +1737,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1671,10 +1796,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1684,12 +1809,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1771,7 +1893,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1794,41 +1916,40 @@ 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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/72e928d8684788d7e2ce03c74420ebb4161a34.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/72e928d8684788d7e2ce03c74420ebb4161a34.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/9c/72e928d8684788d7e2ce03c74420ebb4161a34.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/51d67e81c92a8a7e6b2ed01747b758b1e69401.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/51d67e81c92a8a7e6b2ed01747b758b1e69401.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a3/51d67e81c92a8a7e6b2ed01747b758b1e69401.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/387ae39c95afbe4befdb9e3933132ba53e2d90.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/387ae39c95afbe4befdb9e3933132ba53e2d90.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e5/387ae39c95afbe4befdb9e3933132ba53e2d90.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/5765ece15bff205f82eeb934bb7b4e073ce748.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/5765ece15bff205f82eeb934bb7b4e073ce748.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a1/5765ece15bff205f82eeb934bb7b4e073ce748.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a0566e15576f9fe8e80a494712786ba3c8fe68.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a0566e15576f9fe8e80a494712786ba3c8fe68.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a0566e15576f9fe8e80a494712786ba3c8fe68.debug debian/samtools/usr/bin/md5fa
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a8083b3802efac5bc7e07dde5979d26a71f3ee.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a8083b3802efac5bc7e07dde5979d26a71f3ee.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/27/a8083b3802efac5bc7e07dde5979d26a71f3ee.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/70
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/70/0615f164e9cef36442053fb1e9b67981627f49.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/70/0615f164e9cef36442053fb1e9b67981627f49.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/cb/a71058097fafe99436e6ce9a95ee8ef2fd777d.debug debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/70/0615f164e9cef36442053fb1e9b67981627f49.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
@@ -1836,13 +1957,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/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)
+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-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools 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/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 -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=27a0566e15576f9fe8e80a494712786ba3c8fe68 27a8083b3802efac5bc7e07dde5979d26a71f3ee 700615f164e9cef36442053fb1e9b679 [...]
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
@@ -1861,17 +1982,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_kfreebsd-i386.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_kfreebsd-i386.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_kfreebsd-i386.deb'.
- dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.3-1_kfreebsd-i386.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.3.1-1_kfreebsd-i386.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1625
+Build finished at 20160426-1235
Finished
────────
@@ -1888,108 +2009,99 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_kfreebsd-i386.changes:
-─────────────────────────────────────
+samtools_1.3.1-1_kfreebsd-i386.changes:
+───────────────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-i386
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 82a33127c140bbec5daae39e5f171e9465f6a66b 425886 samtools-dbgsym_1.3-1_kfreebsd-i386.deb
- dd903590521e1b6a53651ca3098d0710feff1352 253940 samtools_1.3-1_kfreebsd-i386.deb
+ 0ff54aeef1cf5063ee25fd1d60b4601375565c96 434644 samtools-dbgsym_1.3.1-1_kfreebsd-i386.deb
+ 1cd6dd34d8031cc8d44aaf20a40231d2f4f3a703 258530 samtools_1.3.1-1_kfreebsd-i386.deb
Checksums-Sha256:
- 63de29f1513133fce4fe1f38a55f9fdb7ca9ea12825986bbbaa277f9b5dbd4e6 425886 samtools-dbgsym_1.3-1_kfreebsd-i386.deb
- 192ffa1d1c1817f36a63bdc962631aceb75d5f472ae69f5d20ab38f0b1a7c543 253940 samtools_1.3-1_kfreebsd-i386.deb
+ 50da067760c4fa4da7bcc4a144180836d8b7aa4f36c0ff0a8ec6aec680d05fb8 434644 samtools-dbgsym_1.3.1-1_kfreebsd-i386.deb
+ 91531f3762bf6f1277183200d32f3cf6757534a228b9ad3d5c32d0116b95fb61 258530 samtools_1.3.1-1_kfreebsd-i386.deb
Files:
- a1eeb754d251384ac2c6ecdccc20c499 425886 debug extra samtools-dbgsym_1.3-1_kfreebsd-i386.deb
- fedf67a33751f10ec87f63a19e79cdd9 253940 science optional samtools_1.3-1_kfreebsd-i386.deb
+ a7a8dba7dafe828e9f56f71dcd38cc44 434644 debug extra samtools-dbgsym_1.3.1-1_kfreebsd-i386.deb
+ 1c6c92bd907e574398027dac7d5af5b9 258530 science optional samtools_1.3.1-1_kfreebsd-i386.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_kfreebsd-i386.deb
-───────────────────────────────────────
+samtools-dbgsym_1.3.1-1_kfreebsd-i386.deb
+─────────────────────────────────────────
new debian package, version 2.0.
- size 425886 bytes: control archive=822 bytes.
- 654 bytes, 13 lines control
+ size 434644 bytes: control archive=824 bytes.
+ 658 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 480
- Depends: samtools (= 1.3-1)
+ Installed-Size: 488
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-────────────────────────────────
+ Build-Ids: 27a0566e15576f9fe8e80a494712786ba3c8fe68 27a8083b3802efac5bc7e07dde5979d26a71f3ee 700615f164e9cef36442053fb1e9b67981627f49 9c72e928d8684788d7e2ce03c74420ebb4161a34 a15765ece15bff205f82eeb934bb7b4e073ce748 a351d67e81c92a8a7e6b2ed01747b758b1e69401 e5387ae39c95afbe4befdb9e3933132ba53e2d90
+
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/27/
+-rw-r--r-- root/root 9552 2016-04-26 12:35 ./usr/lib/debug/.build-id/27/a0566e15576f9fe8e80a494712786ba3c8fe68.debug
+-rw-r--r-- root/root 7084 2016-04-26 12:35 ./usr/lib/debug/.build-id/27/a8083b3802efac5bc7e07dde5979d26a71f3ee.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/70/
+-rw-r--r-- root/root 16912 2016-04-26 12:35 ./usr/lib/debug/.build-id/70/0615f164e9cef36442053fb1e9b67981627f49.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/9c/
+-rw-r--r-- root/root 409952 2016-04-26 12:35 ./usr/lib/debug/.build-id/9c/72e928d8684788d7e2ce03c74420ebb4161a34.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/a1/
+-rw-r--r-- root/root 9452 2016-04-26 12:35 ./usr/lib/debug/.build-id/a1/5765ece15bff205f82eeb934bb7b4e073ce748.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/a3/
+-rw-r--r-- root/root 18160 2016-04-26 12:35 ./usr/lib/debug/.build-id/a3/51d67e81c92a8a7e6b2ed01747b758b1e69401.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/lib/debug/.build-id/e5/
+-rw-r--r-- root/root 9464 2016-04-26 12:35 ./usr/lib/debug/.build-id/e5/387ae39c95afbe4befdb9e3933132ba53e2d90.debug
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/doc/
+lrwxrwxr-x root/root 0 2016-04-26 12:35 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_kfreebsd-i386.deb
+──────────────────────────────────
new debian package, version 2.0.
- size 253940 bytes: control archive=1644 bytes.
+ size 258530 bytes: control archive=1646 bytes.
820 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: kfreebsd-i386
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 716
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 727
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2002,48 +2114,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/bin/
+-rwxr-xr-x root/root 17956 2016-04-26 12:35 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9748 2016-04-26 12:35 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9748 2016-04-26 12:35 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9768 2016-04-26 12:35 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5636 2016-04-26 12:35 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 457284 2016-04-26 12:35 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22116 2016-04-26 12:35 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 12:35 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 12:35 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 12:35 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 12:35 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 12:35 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2063,23 +2175,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-i386
-Build-Space: 17088
-Build-Time: 105
+Build-Space: 17172
+Build-Time: 110
Distribution: sid
Host Architecture: kfreebsd-i386
-Install-Time: 16
-Job: samtools_1.3-1
+Install-Time: 27
+Job: samtools_1.3.1-1
Machine Architecture: kfreebsd-i386
Package: samtools
-Package-Time: 155
-Source-Version: 1.3-1
-Space: 17088
+Package-Time: 171
+Source-Version: 1.3.1-1
+Space: 17172
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1625
-Build needed 00:02:35, 17088k disc space
+Finished at 20160426-1235
+Build needed 00:02:51, 17172k disc space
Signature with key 'E3D16566' requested:
- signfile /home/buildd/build/samtools_1.3-1_kfreebsd-i386.changes E3D16566
+ signfile /home/buildd/build/samtools_1.3.1-1_kfreebsd-i386.changes E3D16566
Successfully signed changes file
diff --git a/m68k.log b/m68k.log
index 08fee77..20440f9 100644
--- a/m68k.log
+++ b/m68k.log
@@ -1,50 +1,41 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs91.physik.fu-berlin.de
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs90.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (m68k) 05 Feb 2016 17:33 ║
+║ samtools 1.3.1-1 (m68k) 26 Apr 2016 15:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: m68k
Build Architecture: m68k
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-gwkHYg/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-gwkHYg' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-m68k-sbuild-72e30027-8cdf-498e-b5e1-4b300e6a8680' 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)
+Get:1 http://incoming.debian-ports.org/buildd unstable InRelease [43.3 kB]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:3 ftp://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable InRelease [39.0 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unreleased InRelease [54.6 kB]
+Get:6 http://incoming.debian-ports.org/buildd unstable/main m68k Packages [72.4 kB]
+Get:7 ftp://ftp.debian.org/debian unstable/main Sources.diff/Index [27.9 kB]
+Get:8 ftp://ftp.debian.org/debian unstable/main Sources 2016-04-25-2052.09.pdiff [23.1 kB]
+Get:9 ftp://ftp.debian.org/debian unstable/main Sources 2016-04-26-0248.52.pdiff [8714 B]
+Get:10 ftp://ftp.debian.org/debian unstable/main Sources 2016-04-26-0848.19.pdiff [4783 B]
+Get:10 ftp://ftp.debian.org/debian unstable/main Sources 2016-04-26-0848.19.pdiff [4783 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [103 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main m68k Packages [14.0 MB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main all Packages [6980 kB]
+Fetched 21.6 MB in 2min 2s (177 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -62,18 +53,16 @@ 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
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)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 2s (1593 kB/s)
Download complete and in download only mode
Check architectures
@@ -85,19 +74,19 @@ 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
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-RWy_FT/apt_archive/sbuild-build-depends-core-dummy.deb'.
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]
+Get:1 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-RWy_FT/apt_archive ./ Packages [524 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-RWy_FT/apt_archive/./Release.gpg: Signature by key 1DEEDC06FCFECEFF54F8EE0DF5A181D302D8662C uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -119,30 +108,30 @@ Recommended packages:
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]
+0 upgraded, 9 newly installed, 0 to remove and 3 not upgraded.
+Need to get 8898 kB/8899 kB of archives.
+After this operation, 38.3 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-RWy_FT/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 5.22.1-10 [2696 kB]
+Get:3 ftp://ftp.debian-ports.org/debian unstable/main m68k libperl5.22 m68k 5.22.1-10 [3243 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main m68k perl m68k 5.22.1-10 [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)
+Fetched 8898 kB in 28s (317 kB/s)
Selecting previously unselected package perl-modules-5.22.
-(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 ... 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) ...
+(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 ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 10395 files and directories currently installed.)
+Preparing to unpack .../perl-modules-5.22_5.22.1-10_all.deb ...
+Unpacking perl-modules-5.22 (5.22.1-10) ...
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) ...
+Preparing to unpack .../libperl5.22_5.22.1-10_m68k.deb ...
+Unpacking libperl5.22:m68k (5.22.1-10) ...
Selecting previously unselected package perl.
-Preparing to unpack .../perl_5.22.1-5_m68k.deb ...
-Unpacking perl (5.22.1-5) ...
+Preparing to unpack .../perl_5.22.1-10_m68k.deb ...
+Unpacking perl (5.22.1-10) ...
Selecting previously unselected package libdpkg-perl.
Preparing to unpack .../libdpkg-perl_1.18.4_all.deb ...
Unpacking libdpkg-perl (1.18.4) ...
@@ -161,9 +150,10 @@ 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) ...
+Processing triggers for libc-bin (2.22-6) ...
+Setting up perl-modules-5.22 (5.22.1-10) ...
+Setting up libperl5.22:m68k (5.22.1-10) ...
+Setting up perl (5.22.1-10) ...
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) ...
@@ -172,23 +162,23 @@ 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) ...
+Processing triggers for libc-bin (2.22-6) ...
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
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-6JSLI3/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
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]
+Get:1 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-6JSLI3/apt_archive ./ Packages [745 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-6JSLI3/apt_archive/./Release.gpg: Signature by key 1DEEDC06FCFECEFF54F8EE0DF5A181D302D8662C uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -200,79 +190,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 3 not upgraded.
+Need to get 24.2 MB/24.2 MB of archives.
+After this operation, 85.0 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-6JSLI3/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 1:2.1-4.3 [178 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]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main m68k libbsd0 m68k 0.8.3-1 [80.7 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable/main m68k bsdmainutils m68k 9.0.10 [176 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unstable/main m68k libpipeline1 m68k 1.4.1-2 [24.3 kB]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main m68k man-db m68k 2.7.5-1 [988 kB]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main m68k autoconf-archive all 20150925-1 [688 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main m68k libsigsegv2 m68k 2.10-4 [28.0 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main m68k libunistring0 m68k 0.9.3-5.2 [255 kB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main m68k libssl1.0.2 m68k 1.0.2g-2 [904 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main m68k libmagic1 m68k 1:5.25-2 [250 kB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main m68k file m68k 1:5.25-2 [60.7 kB]
+Get:14 ftp://ftp.debian-ports.org/debian unstable/main m68k gettext-base m68k 0.19.6-1 [119 kB]
+Get:15 ftp://ftp.debian-ports.org/debian unstable/main m68k libnettle6 m68k 3.2-1 [193 kB]
+Get:16 ftp://ftp.debian-ports.org/debian unstable/main m68k libhogweed4 m68k 3.2-1 [126 kB]
+Get:17 ftp://ftp.debian-ports.org/debian unstable/main m68k libidn11 m68k 1.32-3 [110 kB]
+Get:18 ftp://ftp.debian-ports.org/debian unstable/main m68k libffi6 m68k 3.2.1-4 [17.1 kB]
+Get:19 ftp://ftp.debian-ports.org/debian unstable/main m68k libp11-kit0 m68k 0.23.2-3 [96.8 kB]
+Get:20 ftp://ftp.debian-ports.org/debian unstable/main m68k libtasn1-6 m68k 4.8-1 [44.6 kB]
+Get:21 ftp://ftp.debian-ports.org/debian unstable/main m68k libgnutls30 m68k 3.4.10-3 [678 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main m68k libkeyutils1 m68k 1.5.9-8 [11.3 kB]
+Get:23 ftp://ftp.debian-ports.org/debian unstable/main m68k libkrb5support0 m68k 1.13.2+dfsg-5 [56.7 kB]
+Get:24 ftp://ftp.debian-ports.org/debian unstable/main m68k libk5crypto3 m68k 1.13.2+dfsg-5 [99.1 kB]
+Get:25 ftp://ftp.debian-ports.org/debian unstable/main m68k libkrb5-3 m68k 1.13.2+dfsg-5 [267 kB]
+Get:26 ftp://ftp.debian-ports.org/debian unstable/main m68k libgssapi-krb5-2 m68k 1.13.2+dfsg-5 [130 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main m68k libsasl2-modules-db m68k 2.1.26.dfsg1-15 [64.7 kB]
+Get:28 ftp://ftp.debian-ports.org/debian unstable/main m68k libsasl2-2 m68k 2.1.26.dfsg1-15 [94.9 kB]
+Get:29 ftp://ftp.debian-ports.org/debian unstable/main m68k libldap-2.4-2 m68k 2.4.42+dfsg-2+b2 [199 kB]
+Get:30 ftp://ftp.debian-ports.org/debian unstable/main m68k libicu55 m68k 55.1-7 [7359 kB]
+Get:31 ftp://ftp.debian-ports.org/debian unstable/main m68k libxml2 m68k 2.9.3+dfsg1-1 [788 kB]
+Get:32 ftp://ftp.debian-ports.org/debian unstable/main m68k m4 m68k 1.4.17-5 [238 kB]
+Get:33 ftp://ftp.debian-ports.org/debian unstable/main m68k autoconf all 2.69-10 [338 kB]
+Get:34 ftp://ftp.debian-ports.org/debian unstable/main m68k autotools-dev all 20150820.1 [71.7 kB]
+Get:35 ftp://ftp.debian-ports.org/debian unstable/main m68k automake all 1:1.15-4 [735 kB]
+Get:36 ftp://ftp.debian-ports.org/debian unstable/main m68k autopoint all 0.19.7-2 [424 kB]
+Get:37 ftp://ftp.debian-ports.org/debian unstable/main m68k libglib2.0-0 m68k 2.46.2-1 [2506 kB]
+Get:38 ftp://ftp.debian-ports.org/debian unstable/main m68k libcroco3 m68k 0.6.11-1 [133 kB]
+Get:39 ftp://ftp.debian-ports.org/debian unstable/main m68k gettext m68k 0.19.6-1 [1376 kB]
+Get:40 ftp://ftp.debian-ports.org/debian unstable/main m68k intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 ftp://ftp.debian-ports.org/debian unstable/main m68k po-debconf all 1.0.19 [249 kB]
+Get:42 ftp://ftp.debian-ports.org/debian unstable/main m68k libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 ftp://ftp.debian-ports.org/debian unstable/main m68k libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 ftp://ftp.debian-ports.org/debian unstable/main m68k libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 ftp://ftp.debian-ports.org/debian unstable/main m68k dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 ftp://ftp.debian-ports.org/debian unstable/main m68k libtool all 2.4.6-0.1 [200 kB]
+Get:47 ftp://ftp.debian-ports.org/debian unstable/main m68k dh-autoreconf all 12 [15.8 kB]
+Get:48 ftp://ftp.debian-ports.org/debian unstable/main m68k debhelper all 9.20160403 [800 kB]
+Get:49 ftp://ftp.debian-ports.org/debian unstable/main m68k libnghttp2-14 m68k 1.9.2-1 [66.4 kB]
+Get:50 ftp://ftp.debian-ports.org/debian unstable/main m68k librtmp1 m68k 2.4+20151223.gitfa8646d-1+b1 [53.8 kB]
+Get:51 ftp://ftp.debian-ports.org/debian unstable/main m68k libssh2-1 m68k 1.5.0-2.1 [122 kB]
+Get:52 ftp://ftp.debian-ports.org/debian unstable/main m68k libcurl3-gnutls m68k 7.47.0-1 [246 kB]
+Get:53 ftp://ftp.debian-ports.org/debian unstable/main m68k libhts1 m68k 1.3.1-1 [216 kB]
+Get:54 ftp://ftp.debian-ports.org/debian unstable/main m68k libhts-dev m68k 1.3.1-1 [271 kB]
+Get:55 ftp://ftp.debian-ports.org/debian unstable/main m68k libio-pty-perl m68k 1:1.08-1.1+b1 [33.6 kB]
+Get:56 ftp://ftp.debian-ports.org/debian unstable/main m68k libtinfo-dev m68k 6.0+20160319-1 [65.5 kB]
+Get:57 ftp://ftp.debian-ports.org/debian unstable/main m68k libncurses5-dev m68k 6.0+20160319-1 [152 kB]
+Get:58 ftp://ftp.debian-ports.org/debian unstable/main m68k tabix m68k 1.3.1-1 [195 kB]
+Get:59 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)
+Fetched 24.2 MB in 2min 7s (189 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12548 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
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 libbsd0:m68k.
+Preparing to unpack .../libbsd0_0.8.3-1_m68k.deb ...
+Unpacking libbsd0:m68k (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_m68k.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_m68k.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:m68k.
Preparing to unpack .../libpipeline1_1.4.1-2_m68k.deb ...
Unpacking libpipeline1:m68k (1.4.1-2) ...
@@ -288,6 +314,9 @@ 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 libssl1.0.2:m68k.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_m68k.deb ...
+Unpacking libssl1.0.2:m68k (1.0.2g-2) ...
Selecting previously unselected package libmagic1:m68k.
Preparing to unpack .../libmagic1_1%3a5.25-2_m68k.deb ...
Unpacking libmagic1:m68k (1:5.25-2) ...
@@ -297,6 +326,51 @@ 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 libnettle6:m68k.
+Preparing to unpack .../libnettle6_3.2-1_m68k.deb ...
+Unpacking libnettle6:m68k (3.2-1) ...
+Selecting previously unselected package libhogweed4:m68k.
+Preparing to unpack .../libhogweed4_3.2-1_m68k.deb ...
+Unpacking libhogweed4:m68k (3.2-1) ...
+Selecting previously unselected package libidn11:m68k.
+Preparing to unpack .../libidn11_1.32-3_m68k.deb ...
+Unpacking libidn11:m68k (1.32-3) ...
+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 libp11-kit0:m68k.
+Preparing to unpack .../libp11-kit0_0.23.2-3_m68k.deb ...
+Unpacking libp11-kit0:m68k (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:m68k.
+Preparing to unpack .../libtasn1-6_4.8-1_m68k.deb ...
+Unpacking libtasn1-6:m68k (4.8-1) ...
+Selecting previously unselected package libgnutls30:m68k.
+Preparing to unpack .../libgnutls30_3.4.10-3_m68k.deb ...
+Unpacking libgnutls30:m68k (3.4.10-3) ...
+Selecting previously unselected package libkeyutils1:m68k.
+Preparing to unpack .../libkeyutils1_1.5.9-8_m68k.deb ...
+Unpacking libkeyutils1:m68k (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:m68k.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_m68k.deb ...
+Unpacking libkrb5support0:m68k (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:m68k.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_m68k.deb ...
+Unpacking libk5crypto3:m68k (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:m68k.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_m68k.deb ...
+Unpacking libkrb5-3:m68k (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:m68k.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_m68k.deb ...
+Unpacking libgssapi-krb5-2:m68k (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:m68k.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_m68k.deb ...
+Unpacking libsasl2-modules-db:m68k (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:m68k.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_m68k.deb ...
+Unpacking libsasl2-2:m68k (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:m68k.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_m68k.deb ...
+Unpacking libldap-2.4-2:m68k (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:m68k.
Preparing to unpack .../libicu55_55.1-7_m68k.deb ...
Unpacking libicu55:m68k (55.1-7) ...
@@ -307,17 +381,17 @@ 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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
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) ...
@@ -334,48 +408,67 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:m68k.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_m68k.deb ...
+Unpacking libnghttp2-14:m68k (1.9.2-1) ...
+Selecting previously unselected package librtmp1:m68k.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_m68k.deb ...
+Unpacking librtmp1:m68k (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:m68k.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_m68k.deb ...
+Unpacking libssh2-1:m68k (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:m68k.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_m68k.deb ...
+Unpacking libcurl3-gnutls:m68k (7.47.0-1) ...
Selecting previously unselected package libhts1:m68k.
-Preparing to unpack .../libhts1_1.3-1_m68k.deb ...
-Unpacking libhts1:m68k (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_m68k.deb ...
+Unpacking libhts1:m68k (1.3.1-1) ...
Selecting previously unselected package libhts-dev:m68k.
-Preparing to unpack .../libhts-dev_1.3-1_m68k.deb ...
-Unpacking libhts-dev:m68k (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_m68k.deb ...
+Unpacking libhts-dev:m68k (1.3.1-1) ...
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) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_m68k.deb ...
+Unpacking libtinfo-dev:m68k (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_m68k.deb ...
+Unpacking libncurses5-dev:m68k (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_m68k.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_m68k.deb ...
+Unpacking tabix (1.3.1-1) ...
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) ...
+Processing triggers for libc-bin (2.22-6) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:m68k (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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) ...
@@ -384,37 +477,59 @@ 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 libssl1.0.2:m68k (1.0.2g-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 libnettle6:m68k (3.2-1) ...
+Setting up libhogweed4:m68k (3.2-1) ...
+Setting up libidn11:m68k (1.32-3) ...
+Setting up libffi6:m68k (3.2.1-4) ...
+Setting up libp11-kit0:m68k (0.23.2-3) ...
+Setting up libtasn1-6:m68k (4.8-1) ...
+Setting up libgnutls30:m68k (3.4.10-3) ...
+Setting up libkeyutils1:m68k (1.5.9-8) ...
+Setting up libkrb5support0:m68k (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:m68k (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:m68k (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:m68k (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:m68k (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:m68k (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:m68k (2.4.42+dfsg-2+b2) ...
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 autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 autopoint (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:m68k (1.3-1) ...
-Setting up libhts-dev:m68k (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:m68k (1.9.2-1) ...
+Setting up librtmp1:m68k (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:m68k (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:m68k (7.47.0-1) ...
+Setting up libhts1:m68k (1.3.1-1) ...
+Setting up libhts-dev:m68k (1.3.1-1) ...
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 libtinfo-dev:m68k (6.0+20160319-1) ...
+Setting up libncurses5-dev:m68k (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:m68k (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-6) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -422,8 +537,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-13 gcc-5_5.3.1-13 libc6-dev_2.22-6 libstdc++-5-dev_5.3.1-13 libstdc++6_5.3.1-13 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.9 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-13 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debian-ports-archive-keyring_201 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -434,12 +549,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -461,22 +576,23 @@ 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_SESSION_ID=sid-m68k-sbuild-72e30027-8cdf-498e-b5e1-4b300e6a8680
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c7578
+XDG_RUNTIME_DIR=/run/user/114
+XDG_SESSION_ID=14807
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
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)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -523,15 +639,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -543,6 +659,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -563,82 +681,82 @@ dh_auto_build -- \
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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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»'
@@ -739,7 +857,7 @@ Unsupported ioctl: cmd=0x40049409
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
+ (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
@@ -762,41 +880,41 @@ Unsupported ioctl: cmd=0x40049409
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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/37d89a77a29951545aed9fa159c5ffd675e267.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/37d89a77a29951545aed9fa159c5ffd675e267.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/37d89a77a29951545aed9fa159c5ffd675e267.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/eb
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/eb/f7a8b921d33860a53b984e1fb1be4db9c15110.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/eb/f7a8b921d33860a53b984e1fb1be4db9c15110.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/eb/f7a8b921d33860a53b984e1fb1be4db9c15110.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/42
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/42/8884d68e5926285fcccdfb9528843af559977c.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/42/8884d68e5926285fcccdfb9528843af559977c.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/42/8884d68e5926285fcccdfb9528843af559977c.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01/1361c4f6add66cafd905a2d31db52cc054e308.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01/1361c4f6add66cafd905a2d31db52cc054e308.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/01/1361c4f6add66cafd905a2d31db52cc054e308.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/39a9d2f090859d373fd4fb13fb85f932c6802b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/39a9d2f090859d373fd4fb13fb85f932c6802b.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/a6/39a9d2f090859d373fd4fb13fb85f932c6802b.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/de35c709e9d25e1ad69ba9816e9923689e8b24.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/de35c709e9d25e1ad69ba9816e9923689e8b24.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/29/de35c709e9d25e1ad69ba9816e9923689e8b24.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3e/778469bc4e7cf28c87db8a1f4445a229cbc15b.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3e/778469bc4e7cf28c87db8a1f4445a229cbc15b.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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/3e/778469bc4e7cf28c87db8a1f4445a229cbc15b.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
@@ -804,14 +922,14 @@ 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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite 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/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite were not linked against ld.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/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 -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=011361c4f6add66cafd905a2d31db52cc054e308 29de35c709e9d25e1ad69ba9816e9923689e8b24 3e778469bc4e7cf28c87db8a1f4445a2 [...]
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
@@ -830,17 +948,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_m68k.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_m68k.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_m68k.deb'.
- dpkg-genchanges -B -mdebian/m68k buildd <buildd-vs91 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3-1_m68k.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_m68k.deb'.
+ dpkg-genchanges -B -mdebian/m68k buildd <buildd-vs90 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3.1-1_m68k.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/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
+Build finished at 20160426-1545
Finished
────────
@@ -857,107 +975,99 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_m68k.changes:
-────────────────────────────
+samtools_1.3.1-1_m68k.changes:
+──────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: m68k
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: debian/m68k buildd <buildd-vs91 at glaubitz.dialup.fu-berlin.de>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: debian/m68k buildd <buildd-vs90 at glaubitz.dialup.fu-berlin.de>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 71fe9c8c0e937239922a9b8e89771243dae239c2 428462 samtools-dbgsym_1.3-1_m68k.deb
- 2c52edcb2549b71faa66aa947dc95ddb1940d611 211086 samtools_1.3-1_m68k.deb
+ d1425ab18d21c8e7eb7b9bb29380877f1a24fbb6 435822 samtools-dbgsym_1.3.1-1_m68k.deb
+ a1f2a8afdec268026c2085f4c8e9b921885af0ca 214832 samtools_1.3.1-1_m68k.deb
Checksums-Sha256:
- b2265f275ead2ffc45bddc6d7a9066eecf9431354a92e2b21a486c1df407d23b 428462 samtools-dbgsym_1.3-1_m68k.deb
- aea7269ce2b4da7b207f831742b0b0fe7618b7e73ecc017811b0b0fc370f3eed 211086 samtools_1.3-1_m68k.deb
+ eacb4018cee9b63c63bc4c97bde8c2168813e40b1bb8320a84add8f07c0925fc 435822 samtools-dbgsym_1.3.1-1_m68k.deb
+ 4103782e3ab218e42fea2b7da33033dcd3babff729dea5ba75e4c8a8e968eaa6 214832 samtools_1.3.1-1_m68k.deb
Files:
- 7c14dea6ff0cfa02926b630573121c0d 428462 debug extra samtools-dbgsym_1.3-1_m68k.deb
- 7ae48f62c21220b34351e60b3ab1bec5 211086 science optional samtools_1.3-1_m68k.deb
+ 82c7c93c78cc7ed6ddaea8f0a5b8314f 435822 debug extra samtools-dbgsym_1.3.1-1_m68k.deb
+ af3ec7d9dcb1ec7c655563d74dfd4787 214832 science optional samtools_1.3.1-1_m68k.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_m68k.deb
-──────────────────────────────
+samtools-dbgsym_1.3.1-1_m68k.deb
+────────────────────────────────
new debian package, version 2.0.
- size 428462 bytes: control archive=822 bytes.
- 645 bytes, 13 lines control
+ size 435822 bytes: control archive=822 bytes.
+ 649 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: m68k
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 483
- Depends: samtools (= 1.3-1)
+ Installed-Size: 490
+ Depends: samtools (= 1.3.1-1)
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
+ Build-Ids: 011361c4f6add66cafd905a2d31db52cc054e308 29de35c709e9d25e1ad69ba9816e9923689e8b24 3e778469bc4e7cf28c87db8a1f4445a229cbc15b 428884d68e5926285fcccdfb9528843af559977c 7e37d89a77a29951545aed9fa159c5ffd675e267 a639a9d2f090859d373fd4fb13fb85f932c6802b ebf7a8b921d33860a53b984e1fb1be4db9c15110
-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
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/01/
+-rw-r--r-- root/root 9236 2016-04-26 15:44 ./usr/lib/debug/.build-id/01/1361c4f6add66cafd905a2d31db52cc054e308.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/29/
+-rw-r--r-- root/root 6948 2016-04-26 15:44 ./usr/lib/debug/.build-id/29/de35c709e9d25e1ad69ba9816e9923689e8b24.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/3e/
+-rw-r--r-- root/root 16624 2016-04-26 15:44 ./usr/lib/debug/.build-id/3e/778469bc4e7cf28c87db8a1f4445a229cbc15b.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/42/
+-rw-r--r-- root/root 9244 2016-04-26 15:44 ./usr/lib/debug/.build-id/42/8884d68e5926285fcccdfb9528843af559977c.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/7e/
+-rw-r--r-- root/root 410076 2016-04-26 15:44 ./usr/lib/debug/.build-id/7e/37d89a77a29951545aed9fa159c5ffd675e267.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/a6/
+-rw-r--r-- root/root 9296 2016-04-26 15:44 ./usr/lib/debug/.build-id/a6/39a9d2f090859d373fd4fb13fb85f932c6802b.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/lib/debug/.build-id/eb/
+-rw-r--r-- root/root 18960 2016-04-26 15:44 ./usr/lib/debug/.build-id/eb/f7a8b921d33860a53b984e1fb1be4db9c15110.debug
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 15:44 ./usr/share/doc/samtools-dbgsym -> samtools
-samtools_1.3-1_m68k.deb
-───────────────────────
+samtools_1.3.1-1_m68k.deb
+─────────────────────────
new debian package, version 2.0.
- size 211086 bytes: control archive=1642 bytes.
- 805 bytes, 17 lines control
+ size 214832 bytes: control archive=1639 bytes.
+ 807 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: m68k
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 636
+ Installed-Size: 651
Depends: libc6 (>= 2.7), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
@@ -971,48 +1081,48 @@ samtools_1.3-1_m68k.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 2016-02-05 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
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/bin/
+-rwxr-xr-x root/root 17824 2016-04-26 15:44 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 11:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 11:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 11:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 11:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9620 2016-04-26 15:44 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9620 2016-04-26 15:44 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9640 2016-04-26 15:44 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9604 2016-04-26 15:44 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 11:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 11:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 11:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 11:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 379356 2016-04-26 15:44 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 11:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 11:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 11:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 11:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17900 2016-04-26 15:44 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 11:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 11:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 11:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 13:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 13:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 14:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 13:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 13:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 13:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 15:44 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 15:44 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 15:44 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 15:44 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 15:44 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1032,23 +1142,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: m68k
-Build-Space: 16184
-Build-Time: 583
+Build-Space: 16284
+Build-Time: 748
Distribution: sid
Host Architecture: m68k
-Install-Time: 245
-Job: samtools_1.3-1
+Install-Time: 389
+Job: samtools_1.3.1-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 937
-Source-Version: 1.3-1
-Space: 16184
+Package-Time: 1299
+Source-Version: 1.3.1-1
+Space: 16284
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-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
+Finished at 20160426-1545
+Build needed 00:21:39, 16284k disc space
+Signature with key '53C4870E' requested:
+ signfile /var/lib/buildd/build/samtools_1.3.1-1_m68k.changes 53C4870E
Successfully signed changes file
diff --git a/mips64el.log b/mips64el.log
index 9eac107..87399c7 100644
--- a/mips64el.log
+++ b/mips64el.log
@@ -1,45 +1,44 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on clash.debian.net
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on thor.debian.net
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (mips64el) 06 Feb 2016 00:35 ║
+║ samtools 1.3.1-1 (mips64el) 26 Apr 2016 21:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mips64el
Build Architecture: mips64el
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-wJ4cDs/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-wJ4cDs' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mips64el-sbuild-0b489f9e-e5a0-4d67-8e49-efae9831610e' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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://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)
+Get:1 http://mirrors.tuna.tsinghua.edu.cn/debian unstable InRelease [196 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main Sources [6767 kB]
+Get:4 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/contrib Sources [48.6 kB]
+Get:5 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/non-free Sources [84.1 kB]
+Get:6 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el Packages [6734 kB]
+Get:7 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/contrib mips64el Packages [40.0 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:9 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [103 kB]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main mips64el Packages [101 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mips64el Packages [1820 B]
+Get:14 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:15 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:16 http://ftp.debian.org/debian unstable/main mips64el Packages [6734 kB]
+Get:17 http://ftp.debian.org/debian unstable/contrib mips64el Packages [40.0 kB]
+Fetched 28.0 MB in 22s (1256 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -57,43 +56,40 @@ 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
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 2s (1722 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 3s (1122 kB/s)
Download complete and in download only mode
Check architectures
───────────────────
-sh: 1: gcc: not found
-sbuild: warning: couldn't determine gcc system type, falling back to default (native compilation)
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-O3tI9s/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-XhEbLl/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-XhEbLl/apt_archive ./ Packages [527 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-XhEbLl/apt_archive/./Release.gpg: Signature by key 5751E91AD2A095BCE3EB7C9BBC676CE8C7F166EE uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -106,31 +102,32 @@ 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 18 not upgraded.
-Need to get 0 B/764 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 52 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-O3tI9s/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
+Get:1 file:/«BUILDDIR»/resolver-XhEbLl/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 ... 12334 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 ... 12358 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 (>= 1.3), 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'.
+Merged Build-Depends: 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: 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-ahjlyc/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Sources [373 B]
+Get:5 file:/«BUILDDIR»/resolver-ahjlyc/apt_archive ./ Packages [634 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-ahjlyc/apt_archive/./Release.gpg: Signature by key 5751E91AD2A095BCE3EB7C9BBC676CE8C7F166EE uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -142,79 +139,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 52 not upgraded.
+Need to get 25.0 MB/25.0 MB of archives.
+After this operation, 93.4 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-ahjlyc/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 1:2.1-4.3 [178 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]
+Get:4 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libbsd0 mips64el 0.8.3-1 [82.7 kB]
+Get:5 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el bsdmainutils mips64el 9.0.10 [188 kB]
+Get:6 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libpipeline1 mips64el 1.4.1-2 [26.6 kB]
+Get:7 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el man-db mips64el 2.7.5-1 [990 kB]
+Get:8 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libssl1.0.2 mips64el 1.0.2g-2 [934 kB]
+Get:10 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libmagic1 mips64el 1:5.25-2 [255 kB]
+Get:11 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el file mips64el 1:5.25-2 [61.9 kB]
+Get:12 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el gettext-base mips64el 0.19.7-2 [115 kB]
+Get:13 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libnettle6 mips64el 3.2-1 [204 kB]
+Get:14 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libhogweed4 mips64el 3.2-1 [130 kB]
+Get:15 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libidn11 mips64el 1.32-3 [112 kB]
+Get:16 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libffi6 mips64el 3.2.1-4 [20.7 kB]
+Get:17 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libp11-kit0 mips64el 0.23.2-3 [90.8 kB]
+Get:18 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtasn1-6 mips64el 4.8-1 [47.4 kB]
+Get:19 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libgnutls30 mips64el 3.4.11-3 [685 kB]
+Get:20 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libkeyutils1 mips64el 1.5.9-7 [11.8 kB]
+Get:21 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libkrb5support0 mips64el 1.13.2+dfsg-5 [58.5 kB]
+Get:22 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libk5crypto3 mips64el 1.13.2+dfsg-5 [120 kB]
+Get:23 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libkrb5-3 mips64el 1.13.2+dfsg-5 [275 kB]
+Get:24 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libgssapi-krb5-2 mips64el 1.13.2+dfsg-5 [138 kB]
+Get:25 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libsasl2-modules-db mips64el 2.1.26.dfsg1-15 [66.2 kB]
+Get:26 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libsasl2-2 mips64el 2.1.26.dfsg1-15 [99.6 kB]
+Get:27 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libldap-2.4-2 mips64el 2.4.42+dfsg-2+b2 [203 kB]
+Get:28 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libicu55 mips64el 55.1-7 [7576 kB]
+Get:29 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libxml2 mips64el 2.9.3+dfsg1-1 [830 kB]
+Get:30 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libsigsegv2 mips64el 2.10-5 [28.9 kB]
+Get:31 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el m4 mips64el 1.4.17-5 [253 kB]
+Get:32 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autoconf all 2.69-10 [338 kB]
+Get:33 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autotools-dev all 20150820.1 [71.7 kB]
+Get:34 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el automake all 1:1.15-4 [735 kB]
+Get:35 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el autopoint all 0.19.7-2 [424 kB]
+Get:36 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libglib2.0-0 mips64el 2.48.0-1 [2539 kB]
+Get:37 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libcroco3 mips64el 0.6.11-1 [131 kB]
+Get:38 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libunistring0 mips64el 0.9.3-5.2+b1 [258 kB]
+Get:39 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el gettext mips64el 0.19.7-2 [1445 kB]
+Get:40 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el po-debconf all 1.0.19 [249 kB]
+Get:42 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el dh-autoreconf all 12 [15.8 kB]
+Get:48 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el debhelper all 9.20160403 [800 kB]
+Get:49 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libnghttp2-14 mips64el 1.9.2-1 [72.0 kB]
+Get:50 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el librtmp1 mips64el 2.4+20151223.gitfa8646d-1+b1 [56.0 kB]
+Get:51 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libssh2-1 mips64el 1.5.0-2.1 [129 kB]
+Get:52 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libcurl3-gnutls mips64el 7.47.0-1 [255 kB]
+Get:53 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libhts1 mips64el 1.3.1-1 [237 kB]
+Get:54 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libhts-dev mips64el 1.3.1-1 [342 kB]
+Get:55 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libio-pty-perl mips64el 1:1.08-1.1+b1 [31.6 kB]
+Get:56 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libtinfo-dev mips64el 6.0+20160319-1 [83.5 kB]
+Get:57 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el libncurses5-dev mips64el 6.0+20160319-1 [184 kB]
+Get:58 http://mirrors.tuna.tsinghua.edu.cn/debian unstable/main mips64el tabix mips64el 1.3.1-1 [249 kB]
+Get:59 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 20.5 MB in 1s (10.7 MB/s)
+Fetched 25.0 MB in 4s (6067 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(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) ...
+(Reading database ...
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(Reading database ... 12358 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_mips64el.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:mips64el.
+Preparing to unpack .../libbsd0_0.8.3-1_mips64el.deb ...
+Unpacking libbsd0:mips64el (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b2_mips64el.deb ...
-Unpacking bsdmainutils (9.0.6+b2) ...
+Preparing to unpack .../bsdmainutils_9.0.10_mips64el.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:mips64el.
Preparing to unpack .../libpipeline1_1.4.1-2_mips64el.deb ...
Unpacking libpipeline1:mips64el (1.4.1-2) ...
@@ -224,6 +257,9 @@ 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 libssl1.0.2:mips64el.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_mips64el.deb ...
+Unpacking libssl1.0.2:mips64el (1.0.2g-2) ...
Selecting previously unselected package libmagic1:mips64el.
Preparing to unpack .../libmagic1_1%3a5.25-2_mips64el.deb ...
Unpacking libmagic1:mips64el (1:5.25-2) ...
@@ -233,6 +269,51 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_mips64el.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:mips64el.
+Preparing to unpack .../libnettle6_3.2-1_mips64el.deb ...
+Unpacking libnettle6:mips64el (3.2-1) ...
+Selecting previously unselected package libhogweed4:mips64el.
+Preparing to unpack .../libhogweed4_3.2-1_mips64el.deb ...
+Unpacking libhogweed4:mips64el (3.2-1) ...
+Selecting previously unselected package libidn11:mips64el.
+Preparing to unpack .../libidn11_1.32-3_mips64el.deb ...
+Unpacking libidn11:mips64el (1.32-3) ...
+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 libp11-kit0:mips64el.
+Preparing to unpack .../libp11-kit0_0.23.2-3_mips64el.deb ...
+Unpacking libp11-kit0:mips64el (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:mips64el.
+Preparing to unpack .../libtasn1-6_4.8-1_mips64el.deb ...
+Unpacking libtasn1-6:mips64el (4.8-1) ...
+Selecting previously unselected package libgnutls30:mips64el.
+Preparing to unpack .../libgnutls30_3.4.11-3_mips64el.deb ...
+Unpacking libgnutls30:mips64el (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:mips64el.
+Preparing to unpack .../libkeyutils1_1.5.9-7_mips64el.deb ...
+Unpacking libkeyutils1:mips64el (1.5.9-7) ...
+Selecting previously unselected package libkrb5support0:mips64el.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_mips64el.deb ...
+Unpacking libkrb5support0:mips64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:mips64el.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_mips64el.deb ...
+Unpacking libk5crypto3:mips64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:mips64el.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_mips64el.deb ...
+Unpacking libkrb5-3:mips64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:mips64el.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_mips64el.deb ...
+Unpacking libgssapi-krb5-2:mips64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:mips64el.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_mips64el.deb ...
+Unpacking libsasl2-modules-db:mips64el (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:mips64el.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_mips64el.deb ...
+Unpacking libsasl2-2:mips64el (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:mips64el.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_mips64el.deb ...
+Unpacking libldap-2.4-2:mips64el (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:mips64el.
Preparing to unpack .../libicu55_55.1-7_mips64el.deb ...
Unpacking libicu55:mips64el (55.1-7) ...
@@ -240,26 +321,26 @@ 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) ...
+Preparing to unpack .../libsigsegv2_2.10-5_mips64el.deb ...
+Unpacking libsigsegv2:mips64el (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:mips64el.
-Preparing to unpack .../libglib2.0-0_2.46.2-3_mips64el.deb ...
-Unpacking libglib2.0-0:mips64el (2.46.2-3) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_mips64el.deb ...
+Unpacking libglib2.0-0:mips64el (2.48.0-1) ...
Selecting previously unselected package libcroco3:mips64el.
Preparing to unpack .../libcroco3_0.6.11-1_mips64el.deb ...
Unpacking libcroco3:mips64el (0.6.11-1) ...
@@ -276,87 +357,128 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:mips64el.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_mips64el.deb ...
+Unpacking libnghttp2-14:mips64el (1.9.2-1) ...
+Selecting previously unselected package librtmp1:mips64el.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_mips64el.deb ...
+Unpacking librtmp1:mips64el (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:mips64el.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_mips64el.deb ...
+Unpacking libssh2-1:mips64el (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:mips64el.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_mips64el.deb ...
+Unpacking libcurl3-gnutls:mips64el (7.47.0-1) ...
Selecting previously unselected package libhts1:mips64el.
-Preparing to unpack .../libhts1_1.3-1_mips64el.deb ...
-Unpacking libhts1:mips64el (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_mips64el.deb ...
+Unpacking libhts1:mips64el (1.3.1-1) ...
Selecting previously unselected package libhts-dev:mips64el.
-Preparing to unpack .../libhts-dev_1.3-1_mips64el.deb ...
-Unpacking libhts-dev:mips64el (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_mips64el.deb ...
+Unpacking libhts-dev:mips64el (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:mips64el.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_mips64el.deb ...
-Unpacking libtinfo-dev:mips64el (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_mips64el.deb ...
+Unpacking libtinfo-dev:mips64el (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_mips64el.deb ...
+Unpacking libncurses5-dev:mips64el (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.3-1_mips64el.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_mips64el.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-5) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b2) ...
+Setting up libbsd0:mips64el (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:mips64el (1.0.2g-2) ...
Setting up libmagic1:mips64el (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:mips64el (3.2-1) ...
+Setting up libhogweed4:mips64el (3.2-1) ...
+Setting up libidn11:mips64el (1.32-3) ...
+Setting up libffi6:mips64el (3.2.1-4) ...
+Setting up libp11-kit0:mips64el (0.23.2-3) ...
+Setting up libtasn1-6:mips64el (4.8-1) ...
+Setting up libgnutls30:mips64el (3.4.11-3) ...
+Setting up libkeyutils1:mips64el (1.5.9-7) ...
+Setting up libkrb5support0:mips64el (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:mips64el (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:mips64el (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:mips64el (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:mips64el (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:mips64el (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:mips64el (2.4.42+dfsg-2+b2) ...
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 libsigsegv2:mips64el (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:mips64el (2.48.0-1) ...
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 (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:mips64el (1.3-1) ...
-Setting up libhts-dev:mips64el (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:mips64el (1.9.2-1) ...
+Setting up librtmp1:mips64el (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:mips64el (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:mips64el (7.47.0-1) ...
+Setting up libhts1:mips64el (1.3.1-1) ...
+Setting up libhts-dev:mips64el (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:mips64el (6.0+20160319-1) ...
+Setting up libncurses5-dev:mips64el (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:mips64el (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-5) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -364,8 +486,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-5 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_4.4.6-1
+Package versions: adduser_3.114 apt_1.2.9 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_12.2 bzip2_1.0.6-8+b1 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-11 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -403,7 +525,7 @@ SCHROOT_CHROOT_NAME=sid-mips64el-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=114
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mips64el-sbuild-4e109306-d423-4cd8-8e9e-0873066db43f
+SCHROOT_SESSION_ID=sid-mips64el-sbuild-0b489f9e-e5a0-4d67-8e49-efae9831610e
SCHROOT_UID=109
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -413,11 +535,11 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture mips64el
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -464,15 +586,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -484,6 +606,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,66 +628,66 @@ dh_auto_build -- \
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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
@@ -587,40 +711,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j4 test BGZIP=/usr/bin/bgzip
+ make -j4 test VERBOSE=1 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/fQYixOz32a/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/5oWaHRCGdJ/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/fQYixOz32a/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/5oWaHRCGdJ/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/fQYixOz32a/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/5oWaHRCGdJ/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/fQYixOz32a/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/5oWaHRCGdJ/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -628,7 +752,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/fQYixOz32a/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/5oWaHRCGdJ/dict.fa.gz
.. ok
test_dict:
@@ -636,17 +760,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/fQYixOz32a/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/5oWaHRCGdJ/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/fQYixOz32a/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/5oWaHRCGdJ/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/fQYixOz32a/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/5oWaHRCGdJ/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -654,35 +778,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/fQYixOz32a/mpileup.bam.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/5oWaHRCGdJ/mpileup.bam.list -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/5oWaHRCGdJ/mpileup.cram.list -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/5oWaHRCGdJ/mpileup.bam.list -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/5oWaHRCGdJ/mpileup.cram.list -f /tmp/5oWaHRCGdJ/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/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/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/5oWaHRCGdJ/mpileup.cram.list -f /tmp/5oWaHRCGdJ/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/fQYixOz32a/mpileup.cram.list -f /tmp/fQYixOz32a/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/5oWaHRCGdJ/mpileup.cram.list -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5oWaHRCGdJ/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/5oWaHRCGdJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/5oWaHRCGdJ/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -932,41 +1056,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/fQYixOz32a/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/fQYixOz32a/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/5oWaHRCGdJ/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/fQYixOz32a/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/fQYixOz32a/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/5oWaHRCGdJ/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/fQYixOz32a/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/fQYixOz32a/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/5oWaHRCGdJ/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/fQYixOz32a/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/5oWaHRCGdJ/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/fQYixOz32a/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/5oWaHRCGdJ/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -980,419 +1104,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
+
+ 78: Count -l Library 3 (CRAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 140: Region Z (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 141: Count Z (BAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 267: Make CRAM with no UR field .. ok
- 263: CIGAR B-operator removal .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 264: Big SAM -> BAM .. ok
+ 269: CIGAR B-operator removal .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 270: Big SAM -> BAM .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 267: Big SAM -> CRAM .. ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 273: Big SAM -> CRAM .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 280: Subsample 0.5 (BAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 281: Subsample 0.8 (BAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 282: Subsample 0.2 (CRAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1540,7 +1676,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qnHqAQUUUz - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/DZGjETm_0M - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1560,15 +1696,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/5oWaHRCGdJ/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/5oWaHRCGdJ/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fQYixOz32a/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/5oWaHRCGdJ/sorttmp
.. ok
test_fixmate:
@@ -1622,8 +1758,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1671,10 +1817,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1684,12 +1830,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1771,7 +1914,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1794,41 +1937,41 @@ 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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/5bec83836b0f841a48e58062869c8fae3b5954.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/5bec83836b0f841a48e58062869c8fae3b5954.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d6/5bec83836b0f841a48e58062869c8fae3b5954.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ef
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ef/9fde68b90df09b7e711410c39968ed029b38f0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ef/9fde68b90df09b7e711410c39968ed029b38f0.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ef/9fde68b90df09b7e711410c39968ed029b38f0.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6/5680aa023aed42b517c679dc83fd957fafc2df.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6/5680aa023aed42b517c679dc83fd957fafc2df.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e6/5680aa023aed42b517c679dc83fd957fafc2df.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/37756ac1f036ad4f5cbe183e6dcf1d8013fca4.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/37756ac1f036ad4f5cbe183e6dcf1d8013fca4.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/36/37756ac1f036ad4f5cbe183e6dcf1d8013fca4.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/f28bdb3920c95c7f87d911fa82e7d1295a251e.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/f28bdb3920c95c7f87d911fa82e7d1295a251e.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ee/f28bdb3920c95c7f87d911fa82e7d1295a251e.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/12
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/12/8e9e28d4c3043daf5ada68876e2f99edf1eb1d.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/12/8e9e28d4c3043daf5ada68876e2f99edf1eb1d.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/12/8e9e28d4c3043daf5ada68876e2f99edf1eb1d.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ce54e738119226eb6fc4c5a24b482f8200f2fb.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ce54e738119226eb6fc4c5a24b482f8200f2fb.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/ce/f5ba02e2233438e2e5504f9ae3a58cf668aff9.debug debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/cd/ce54e738119226eb6fc4c5a24b482f8200f2fb.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
@@ -1836,13 +1979,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+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-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam 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=5d9cadb7125f183fc6120c97b7ff7870e794675c 78f1d518d33d223cea49a2c6ce104461c506e184 9eec5d307751afab496de7cd7be73f17 [...]
+ 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=128e9e28d4c3043daf5ada68876e2f99edf1eb1d 3637756ac1f036ad4f5cbe183e6dcf1d8013fca4 cdce54e738119226eb6fc4c5a24b482f [...]
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
@@ -1861,17 +2004,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_mips64el.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_mips64el.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_mips64el.deb'.
- dpkg-genchanges -B -mmips64el Build Daemon (clash) <buildd_mips64el-clash at buildd.debian.org> >../samtools_1.3-1_mips64el.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_mips64el.deb'.
+ dpkg-genchanges -B -mmips64el Build Daemon (thor) <buildd_mips64el-thor at buildd.debian.org> >../samtools_1.3.1-1_mips64el.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160206-0133
+Build finished at 20160426-2249
Finished
────────
@@ -1888,108 +2031,100 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_mips64el.changes:
-────────────────────────────────
+samtools_1.3.1-1_mips64el.changes:
+──────────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: mips64el
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: mips64el Build Daemon (clash) <buildd_mips64el-clash at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: mips64el Build Daemon (thor) <buildd_mips64el-thor at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- db1a8257413ce2dabffd584224fda38024ea7b9c 462710 samtools-dbgsym_1.3-1_mips64el.deb
- 4425c2189e5d7fe2e467bc712c801dc9b314d627 240530 samtools_1.3-1_mips64el.deb
+ d7ce841e1ed3ac38c085c9cb22ab360e4d042194 471520 samtools-dbgsym_1.3.1-1_mips64el.deb
+ 8494a8dee057040910d917104676087bf1c3604f 244560 samtools_1.3.1-1_mips64el.deb
Checksums-Sha256:
- 6a3ecd015ccde15b8863f9e42d224d48c8168c796e09a3215141a0e266f72fce 462710 samtools-dbgsym_1.3-1_mips64el.deb
- 7248260663b92e55b697a6c9efebc79699f4449ba2b3c68d0426318ee7c09ba4 240530 samtools_1.3-1_mips64el.deb
+ a794d096243d0a480901ee50306ae1ee2dcd819e892fd24ab5f612797a716aec 471520 samtools-dbgsym_1.3.1-1_mips64el.deb
+ d33904dfd43d61436bd2edeb2c9ef1cedf095ad81efaa9b20dd09974c74e6910 244560 samtools_1.3.1-1_mips64el.deb
Files:
- 733bfe239bb53bb3a22f9e4ec54ba491 462710 debug extra samtools-dbgsym_1.3-1_mips64el.deb
- 06062eae25f2dabedff5f557c3c61871 240530 science optional samtools_1.3-1_mips64el.deb
+ 508f89cc490292931ca7575d9dd2c8a5 471520 debug extra samtools-dbgsym_1.3.1-1_mips64el.deb
+ 6e86526381fd901be9c1364e43413b0a 244560 science optional samtools_1.3.1-1_mips64el.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_mips64el.deb
-──────────────────────────────────
+samtools-dbgsym_1.3.1-1_mips64el.deb
+────────────────────────────────────
new debian package, version 2.0.
- size 462710 bytes: control archive=821 bytes.
- 650 bytes, 13 lines control
+ size 471520 bytes: control archive=820 bytes.
+ 654 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: mips64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1063
- Depends: samtools (= 1.3-1)
+ Installed-Size: 1082
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-───────────────────────────
+ Build-Ids: 128e9e28d4c3043daf5ada68876e2f99edf1eb1d 3637756ac1f036ad4f5cbe183e6dcf1d8013fca4 cdce54e738119226eb6fc4c5a24b482f8200f2fb d65bec83836b0f841a48e58062869c8fae3b5954 e65680aa023aed42b517c679dc83fd957fafc2df eef28bdb3920c95c7f87d911fa82e7d1295a251e ef9fde68b90df09b7e711410c39968ed029b38f0
+
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/12/
+-rw-r--r-- root/root 37736 2016-04-26 22:49 ./usr/lib/debug/.build-id/12/8e9e28d4c3043daf5ada68876e2f99edf1eb1d.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/36/
+-rw-r--r-- root/root 20000 2016-04-26 22:49 ./usr/lib/debug/.build-id/36/37756ac1f036ad4f5cbe183e6dcf1d8013fca4.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/cd/
+-rw-r--r-- root/root 923040 2016-04-26 22:49 ./usr/lib/debug/.build-id/cd/ce54e738119226eb6fc4c5a24b482f8200f2fb.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/d6/
+-rw-r--r-- root/root 51592 2016-04-26 22:49 ./usr/lib/debug/.build-id/d6/5bec83836b0f841a48e58062869c8fae3b5954.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/e6/
+-rw-r--r-- root/root 20768 2016-04-26 22:49 ./usr/lib/debug/.build-id/e6/5680aa023aed42b517c679dc83fd957fafc2df.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/ee/
+-rw-r--r-- root/root 20000 2016-04-26 22:49 ./usr/lib/debug/.build-id/ee/f28bdb3920c95c7f87d911fa82e7d1295a251e.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/lib/debug/.build-id/ef/
+-rw-r--r-- root/root 14504 2016-04-26 22:49 ./usr/lib/debug/.build-id/ef/9fde68b90df09b7e711410c39968ed029b38f0.debug
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 22:49 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_mips64el.deb
+─────────────────────────────
new debian package, version 2.0.
- size 240530 bytes: control archive=1634 bytes.
- 810 bytes, 17 lines control
+ size 244560 bytes: control archive=1635 bytes.
+ 809 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: mips64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 778
- Depends: libc6 (>= 2.21), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 789
+ Depends: libc6 (>= 2.7), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2002,48 +2137,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/bin/
+-rwxr-xr-x root/root 23336 2016-04-26 22:49 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 17:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 17:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 17:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 17:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 11080 2016-04-26 22:49 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 11080 2016-04-26 22:49 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 15112 2016-04-26 22:49 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10912 2016-04-26 22:49 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 17:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 17:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 17:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 17:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 488696 2016-04-26 22:49 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 17:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 17:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 17:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 17:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 36192 2016-04-26 22:49 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 17:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 17:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 17:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 19:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 19:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 20:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 19:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 19:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 19:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 22:49 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 22:49 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 22:49 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 22:49 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 22:49 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2063,19 +2198,19 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mips64el
-Build-Space: 22128
-Build-Time: 3326
+Build-Space: 22240
+Build-Time: 3269
Distribution: sid
Host Architecture: mips64el
-Install-Time: 57
-Job: samtools_1.3-1
+Install-Time: 64
+Job: samtools_1.3.1-1
Machine Architecture: mipsel
Package: samtools
-Package-Time: 3472
-Source-Version: 1.3-1
-Space: 22128
+Package-Time: 3415
+Source-Version: 1.3.1-1
+Space: 22240
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160206-0133
-Build needed 00:57:52, 22128k disc space
+Finished at 20160426-2249
+Build needed 00:56:55, 22240k disc space
diff --git a/mipsel.log b/mipsel.log
index 9f36a52..88a7712 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-aql-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-manda-02.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (mipsel) 05 Feb 2016 17:21 ║
+║ samtools 1.3.1-1 (mipsel) 26 Apr 2016 12:52 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mipsel
Build Architecture: mipsel
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-8FtOtP/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-8FtOtP' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-13cf1f61-23ec-4544-a0b9-0456e11081ec' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.de.debian.org/debian unstable InRelease [196 kB]
+Get:2 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main Sources [6767 kB]
+Get:6 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:7 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:8 http://ftp.debian.org/debian unstable/main mipsel Packages [6873 kB]
+Get:9 http://ftp.debian.org/debian unstable/contrib mipsel Packages [42.0 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/main mipsel Packages [6873 kB]
+Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:15 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:16 http://incoming.debian.org/debian-buildd buildd-unstable/main mipsel Packages [100 kB]
+Get:17 http://incoming.debian.org/debian-buildd buildd-unstable/contrib mipsel Packages [2288 B]
+Get:18 http://ftp.de.debian.org/debian unstable/contrib mipsel Packages [42.0 kB]
+Fetched 28.3 MB in 29s (953 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 0s (7059 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (8170 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,15 @@ 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-b0HCFz/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-LPKaGu/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-LPKaGu/apt_archive ./ Packages [527 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -106,29 +104,28 @@ 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 10 not upgraded.
+0 upgraded, 1 newly installed, 0 to remove and 13 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-b0HCFz/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
+Get:1 file:/«BUILDDIR»/resolver-LPKaGu/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 ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12093 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 ... 12139 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 (>= 4:5.3), 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-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]
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-7WQ6YH/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ Packages [746 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +139,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 13 not upgraded.
+Need to get 25.0 MB/25.0 MB of archives.
+After this operation, 90.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-7WQ6YH/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [996 B]
+Get:2 http://ftp.de.debian.org/debian unstable/main mipsel bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://ftp.de.debian.org/debian unstable/main mipsel groff-base mipsel 1.22.3-7 [1281 kB]
+Get:4 http://ftp.de.debian.org/debian unstable/main mipsel libbsd0 mipsel 0.8.3-1 [99.8 kB]
+Get:5 http://ftp.de.debian.org/debian unstable/main mipsel bsdmainutils mipsel 9.0.10 [186 kB]
+Get:6 http://ftp.de.debian.org/debian unstable/main mipsel libpipeline1 mipsel 1.4.1-2 [27.3 kB]
+Get:7 http://ftp.de.debian.org/debian unstable/main mipsel man-db mipsel 2.7.5-1 [991 kB]
+Get:8 http://ftp.de.debian.org/debian unstable/main mipsel autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://ftp.de.debian.org/debian unstable/main mipsel libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
+Get:10 http://ftp.de.debian.org/debian unstable/main mipsel libssl1.0.2 mipsel 1.0.2g-2 [947 kB]
+Get:11 http://ftp.de.debian.org/debian unstable/main mipsel libmagic1 mipsel 1:5.25-2 [258 kB]
+Get:12 http://ftp.de.debian.org/debian unstable/main mipsel file mipsel 1:5.25-2 [61.6 kB]
+Get:13 http://ftp.de.debian.org/debian unstable/main mipsel gettext-base mipsel 0.19.7-2 [114 kB]
+Get:14 http://ftp.de.debian.org/debian unstable/main mipsel libnettle6 mipsel 3.2-1 [221 kB]
+Get:15 http://ftp.de.debian.org/debian unstable/main mipsel libhogweed4 mipsel 3.2-1 [129 kB]
+Get:16 http://ftp.de.debian.org/debian unstable/main mipsel libidn11 mipsel 1.32-3 [112 kB]
+Get:17 http://ftp.de.debian.org/debian unstable/main mipsel libffi6 mipsel 3.2.1-4 [18.6 kB]
+Get:18 http://ftp.de.debian.org/debian unstable/main mipsel libp11-kit0 mipsel 0.23.2-3 [91.1 kB]
+Get:19 http://ftp.de.debian.org/debian unstable/main mipsel libtasn1-6 mipsel 4.8-1 [47.0 kB]
+Get:20 http://ftp.de.debian.org/debian unstable/main mipsel libgnutls30 mipsel 3.4.11-3 [685 kB]
+Get:21 http://ftp.de.debian.org/debian unstable/main mipsel libkeyutils1 mipsel 1.5.9-8 [11.8 kB]
+Get:22 http://ftp.de.debian.org/debian unstable/main mipsel libkrb5support0 mipsel 1.13.2+dfsg-5 [58.3 kB]
+Get:23 http://ftp.de.debian.org/debian unstable/main mipsel libk5crypto3 mipsel 1.13.2+dfsg-5 [122 kB]
+Get:24 http://ftp.de.debian.org/debian unstable/main mipsel libkrb5-3 mipsel 1.13.2+dfsg-5 [277 kB]
+Get:25 http://ftp.de.debian.org/debian unstable/main mipsel libgssapi-krb5-2 mipsel 1.13.2+dfsg-5 [138 kB]
+Get:26 http://ftp.de.debian.org/debian unstable/main mipsel libsasl2-modules-db mipsel 2.1.26.dfsg1-15 [66.2 kB]
+Get:27 http://ftp.de.debian.org/debian unstable/main mipsel libsasl2-2 mipsel 2.1.26.dfsg1-15 [99.2 kB]
+Get:28 http://ftp.de.debian.org/debian unstable/main mipsel libldap-2.4-2 mipsel 2.4.42+dfsg-2+b2 [203 kB]
+Get:29 http://ftp.de.debian.org/debian unstable/main mipsel libicu55 mipsel 55.1-7 [7586 kB]
+Get:30 http://ftp.de.debian.org/debian unstable/main mipsel libxml2 mipsel 2.9.3+dfsg1-1 [829 kB]
+Get:31 http://ftp.de.debian.org/debian unstable/main mipsel libsigsegv2 mipsel 2.10-5 [28.7 kB]
+Get:32 http://ftp.de.debian.org/debian unstable/main mipsel m4 mipsel 1.4.17-5 [249 kB]
+Get:33 http://ftp.de.debian.org/debian unstable/main mipsel autoconf all 2.69-10 [338 kB]
+Get:34 http://ftp.de.debian.org/debian unstable/main mipsel autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://ftp.de.debian.org/debian unstable/main mipsel automake all 1:1.15-4 [735 kB]
+Get:36 http://ftp.de.debian.org/debian unstable/main mipsel autopoint all 0.19.7-2 [424 kB]
+Get:37 http://ftp.de.debian.org/debian unstable/main mipsel libglib2.0-0 mipsel 2.48.0-1 [2559 kB]
+Get:38 http://ftp.de.debian.org/debian unstable/main mipsel libcroco3 mipsel 0.6.11-1 [131 kB]
+Get:39 http://ftp.de.debian.org/debian unstable/main mipsel gettext mipsel 0.19.7-2 [1451 kB]
+Get:40 http://ftp.de.debian.org/debian unstable/main mipsel intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://ftp.de.debian.org/debian unstable/main mipsel po-debconf all 1.0.19 [249 kB]
+Get:42 http://ftp.de.debian.org/debian unstable/main mipsel libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://ftp.de.debian.org/debian unstable/main mipsel libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://ftp.de.debian.org/debian unstable/main mipsel libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://ftp.de.debian.org/debian unstable/main mipsel dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://ftp.de.debian.org/debian unstable/main mipsel libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://ftp.de.debian.org/debian unstable/main mipsel dh-autoreconf all 12 [15.8 kB]
+Get:48 http://ftp.de.debian.org/debian unstable/main mipsel debhelper all 9.20160403 [800 kB]
+Get:49 http://ftp.de.debian.org/debian unstable/main mipsel libnghttp2-14 mipsel 1.9.2-1 [72.0 kB]
+Get:50 http://ftp.de.debian.org/debian unstable/main mipsel librtmp1 mipsel 2.4+20151223.gitfa8646d-1+b1 [55.8 kB]
+Get:51 http://ftp.de.debian.org/debian unstable/main mipsel libssh2-1 mipsel 1.5.0-2.1 [129 kB]
+Get:52 http://ftp.de.debian.org/debian unstable/main mipsel libcurl3-gnutls mipsel 7.47.0-1 [262 kB]
+Get:53 http://ftp.de.debian.org/debian unstable/main mipsel libhts1 mipsel 1.3.1-1 [240 kB]
+Get:54 http://ftp.de.debian.org/debian unstable/main mipsel libhts-dev mipsel 1.3.1-1 [332 kB]
+Get:55 http://ftp.de.debian.org/debian unstable/main mipsel libio-pty-perl mipsel 1:1.08-1.1+b1 [31.5 kB]
+Get:56 http://ftp.de.debian.org/debian unstable/main mipsel libtinfo-dev mipsel 6.0+20160319-1 [78.8 kB]
+Get:57 http://ftp.de.debian.org/debian unstable/main mipsel libncurses5-dev mipsel 6.0+20160319-1 [177 kB]
+Get:58 http://ftp.de.debian.org/debian unstable/main mipsel tabix mipsel 1.3.1-1 [243 kB]
+Get:59 http://ftp.de.debian.org/debian unstable/main mipsel zlib1g-dev mipsel 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 20.5 MB in 2s (9861 kB/s)
+Fetched 25.0 MB in 2s (9394 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%
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(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) ...
+(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 ... 40%
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(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
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(Reading database ... 75%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12139 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_mipsel.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:mipsel.
+Preparing to unpack .../libbsd0_0.8.3-1_mipsel.deb ...
+Unpacking libbsd0:mipsel (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_mipsel.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_mipsel.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:mipsel.
Preparing to unpack .../libpipeline1_1.4.1-2_mipsel.deb ...
Unpacking libpipeline1:mipsel (1.4.1-2) ...
@@ -224,12 +257,12 @@ 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) ...
+Selecting previously unselected package libssl1.0.2:mipsel.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_mipsel.deb ...
+Unpacking libssl1.0.2:mipsel (1.0.2g-2) ...
Selecting previously unselected package libmagic1:mipsel.
Preparing to unpack .../libmagic1_1%3a5.25-2_mipsel.deb ...
Unpacking libmagic1:mipsel (1:5.25-2) ...
@@ -239,30 +272,78 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../gettext-base_0.19.7-2_mipsel.deb ...
Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:mipsel.
+Preparing to unpack .../libnettle6_3.2-1_mipsel.deb ...
+Unpacking libnettle6:mipsel (3.2-1) ...
+Selecting previously unselected package libhogweed4:mipsel.
+Preparing to unpack .../libhogweed4_3.2-1_mipsel.deb ...
+Unpacking libhogweed4:mipsel (3.2-1) ...
+Selecting previously unselected package libidn11:mipsel.
+Preparing to unpack .../libidn11_1.32-3_mipsel.deb ...
+Unpacking libidn11:mipsel (1.32-3) ...
+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 libp11-kit0:mipsel.
+Preparing to unpack .../libp11-kit0_0.23.2-3_mipsel.deb ...
+Unpacking libp11-kit0:mipsel (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:mipsel.
+Preparing to unpack .../libtasn1-6_4.8-1_mipsel.deb ...
+Unpacking libtasn1-6:mipsel (4.8-1) ...
+Selecting previously unselected package libgnutls30:mipsel.
+Preparing to unpack .../libgnutls30_3.4.11-3_mipsel.deb ...
+Unpacking libgnutls30:mipsel (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:mipsel.
+Preparing to unpack .../libkeyutils1_1.5.9-8_mipsel.deb ...
+Unpacking libkeyutils1:mipsel (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:mipsel.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_mipsel.deb ...
+Unpacking libkrb5support0:mipsel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:mipsel.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_mipsel.deb ...
+Unpacking libk5crypto3:mipsel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:mipsel.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_mipsel.deb ...
+Unpacking libkrb5-3:mipsel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:mipsel.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_mipsel.deb ...
+Unpacking libgssapi-krb5-2:mipsel (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:mipsel.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_mipsel.deb ...
+Unpacking libsasl2-modules-db:mipsel (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:mipsel.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_mipsel.deb ...
+Unpacking libsasl2-2:mipsel (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:mipsel.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_mipsel.deb ...
+Unpacking libldap-2.4-2:mipsel (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:mipsel.
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 libsigsegv2:mipsel.
+Preparing to unpack .../libsigsegv2_2.10-5_mipsel.deb ...
+Unpacking libsigsegv2:mipsel (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:mipsel.
-Preparing to unpack .../libglib2.0-0_2.46.2-3_mipsel.deb ...
-Unpacking libglib2.0-0:mipsel (2.46.2-3) ...
+Preparing to unpack .../libglib2.0-0_2.48.0-1_mipsel.deb ...
+Unpacking libglib2.0-0:mipsel (2.48.0-1) ...
Selecting previously unselected package libcroco3:mipsel.
Preparing to unpack .../libcroco3_0.6.11-1_mipsel.deb ...
Unpacking libcroco3:mipsel (0.6.11-1) ...
@@ -276,87 +357,128 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:mipsel.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_mipsel.deb ...
+Unpacking libnghttp2-14:mipsel (1.9.2-1) ...
+Selecting previously unselected package librtmp1:mipsel.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_mipsel.deb ...
+Unpacking librtmp1:mipsel (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:mipsel.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_mipsel.deb ...
+Unpacking libssh2-1:mipsel (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:mipsel.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_mipsel.deb ...
+Unpacking libcurl3-gnutls:mipsel (7.47.0-1) ...
Selecting previously unselected package libhts1:mipsel.
-Preparing to unpack .../libhts1_1.3-1_mipsel.deb ...
-Unpacking libhts1:mipsel (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_mipsel.deb ...
+Unpacking libhts1:mipsel (1.3.1-1) ...
Selecting previously unselected package libhts-dev:mipsel.
-Preparing to unpack .../libhts-dev_1.3-1_mipsel.deb ...
-Unpacking libhts-dev:mipsel (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_mipsel.deb ...
+Unpacking libhts-dev:mipsel (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:mipsel.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_mipsel.deb ...
-Unpacking libtinfo-dev:mipsel (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_mipsel.deb ...
+Unpacking libtinfo-dev:mipsel (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_mipsel.deb ...
+Unpacking libncurses5-dev:mipsel (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.3-1_mipsel.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_mipsel.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:mipsel (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:mipsel (1.0.2g-2) ...
Setting up libmagic1:mipsel (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:mipsel (3.2-1) ...
+Setting up libhogweed4:mipsel (3.2-1) ...
+Setting up libidn11:mipsel (1.32-3) ...
+Setting up libffi6:mipsel (3.2.1-4) ...
+Setting up libp11-kit0:mipsel (0.23.2-3) ...
+Setting up libtasn1-6:mipsel (4.8-1) ...
+Setting up libgnutls30:mipsel (3.4.11-3) ...
+Setting up libkeyutils1:mipsel (1.5.9-8) ...
+Setting up libkrb5support0:mipsel (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:mipsel (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:mipsel (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:mipsel (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:mipsel (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:mipsel (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:mipsel (2.4.42+dfsg-2+b2) ...
Setting up libicu55:mipsel (55.1-7) ...
Setting up libxml2:mipsel (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:mipsel (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:mipsel (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:mipsel (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:mipsel (1.3-1) ...
-Setting up libhts-dev:mipsel (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:mipsel (1.9.2-1) ...
+Setting up librtmp1:mipsel (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:mipsel (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:mipsel (7.47.0-1) ...
+Setting up libhts1:mipsel (1.3.1-1) ...
+Setting up libhts-dev:mipsel (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:mipsel (6.0+20160319-1) ...
+Setting up libncurses5-dev:mipsel (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -364,8 +486,8 @@ W: No sandbox user '_apt' on the system, can not drop privileges
└──────────────────────────────────────────────────────────────────────────────┘
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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_5.3.1-15 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -403,23 +525,23 @@ SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mipsel-sbuild-ab539df7-da35-49a8-9d8f-c2d942ce0cc8
+SCHROOT_SESSION_ID=sid-mipsel-sbuild-13cf1f61-23ec-4544-a0b9-0456e11081ec
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=c2910
+USERNAME=buildd
+XDG_SESSION_ID=c1
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture mipsel
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -466,15 +588,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -486,6 +608,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -506,66 +630,66 @@ dh_auto_build -- \
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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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
@@ -589,40 +713,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j5 test BGZIP=/usr/bin/bgzip
+ make -j5 test VERBOSE=1 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/0l8Ujf59YU/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/fhsD4FqrKq/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/0l8Ujf59YU/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/fhsD4FqrKq/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/0l8Ujf59YU/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/fhsD4FqrKq/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/0l8Ujf59YU/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/fhsD4FqrKq/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -630,7 +754,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/0l8Ujf59YU/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/fhsD4FqrKq/dict.fa.gz
.. ok
test_dict:
@@ -638,17 +762,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/0l8Ujf59YU/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/fhsD4FqrKq/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/0l8Ujf59YU/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/fhsD4FqrKq/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/0l8Ujf59YU/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/fhsD4FqrKq/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -656,35 +780,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/0l8Ujf59YU/mpileup.bam.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/fhsD4FqrKq/mpileup.bam.list -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/fhsD4FqrKq/mpileup.cram.list -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/fhsD4FqrKq/mpileup.bam.list -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/fhsD4FqrKq/mpileup.cram.list -f /tmp/fhsD4FqrKq/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/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/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/fhsD4FqrKq/mpileup.cram.list -f /tmp/fhsD4FqrKq/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/0l8Ujf59YU/mpileup.cram.list -f /tmp/0l8Ujf59YU/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/fhsD4FqrKq/mpileup.cram.list -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:1050-1060 /tmp/fhsD4FqrKq/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/fhsD4FqrKq/mpileup.ref.fa.gz -r17:1050-1060 /tmp/fhsD4FqrKq/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -934,41 +1058,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/fhsD4FqrKq/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/fhsD4FqrKq/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/fhsD4FqrKq/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/fhsD4FqrKq/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/fhsD4FqrKq/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/fhsD4FqrKq/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/0l8Ujf59YU/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/fhsD4FqrKq/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/0l8Ujf59YU/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/fhsD4FqrKq/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -982,419 +1106,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
+
+ 78: Count -l Library 3 (CRAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 140: Region Z (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 141: Count Z (BAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 267: Make CRAM with no UR field .. ok
- 263: CIGAR B-operator removal .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 264: Big SAM -> BAM .. ok
+ 269: CIGAR B-operator removal .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 270: Big SAM -> BAM .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 267: Big SAM -> CRAM .. ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 273: Big SAM -> CRAM .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 279: Subsample 0.2 (BAM input) ............ ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 280: Subsample 0.5 (BAM input) ............ ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 281: Subsample 0.8 (BAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 282: Subsample 0.2 (CRAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1542,7 +1678,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/PzR_6A1_7E - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/tbPCL82wMZ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1562,15 +1698,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fhsD4FqrKq/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fhsD4FqrKq/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/0l8Ujf59YU/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/fhsD4FqrKq/sorttmp
.. ok
test_fixmate:
@@ -1624,8 +1760,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1641,15 +1787,11 @@ test_reheader:
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:.*//'
-
- ERR:
-.. failed ...
+.. 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:.*//'
-
- ERR:
-.. failed ...
+.. ok
test_addrprg:
/«PKGBUILDDIR»/samtools addreplacerg -O sam -m overwrite_all /«PKGBUILDDIR»/test/addrprg/1_fixup.sam
@@ -1677,29 +1819,377 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 396
- failed .. 2
- expected failure .. 18
+ total .. 423
+ passed .. 403
+ failed .. 0
+ expected failure .. 20
unexpected pass .. 0
-Makefile:201: recipe for target 'test' failed
-make[2]: *** [test] Error 1
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
+
+Expected passes: 124
+Unexpected passes: 0
+Expected failures: 0
+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
+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
+ install -d debian/samtools
+ make -j5 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»'
-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
+ 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\.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
+ 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/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/dbgsym-root/usr/lib/debug/.build-id/60
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/60/f48d480d541c8801acd3797905af369d782ce0.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/60/f48d480d541c8801acd3797905af369d782ce0.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/60/f48d480d541c8801acd3797905af369d782ce0.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/5ced76163a2f5fed790513fdcd8bdb83bb87be.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/fd/5ced76163a2f5fed790513fdcd8bdb83bb87be.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/fd/5ced76163a2f5fed790513fdcd8bdb83bb87be.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a/2dd4fd75b72d0edd68257cee47205328502274.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a/2dd4fd75b72d0edd68257cee47205328502274.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/0a/2dd4fd75b72d0edd68257cee47205328502274.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69/84737eef6436818899c075426bcd61e2015378.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/69/84737eef6436818899c075426bcd61e2015378.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/69/84737eef6436818899c075426bcd61e2015378.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c3
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c3/afeeb9d0b56b65de341debe58d2f2f8e479820.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/c3/afeeb9d0b56b65de341debe58d2f2f8e479820.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/c3/afeeb9d0b56b65de341debe58d2f2f8e479820.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40/5014340a030a0d759a7ab740550e993565f0f6.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40/5014340a030a0d759a7ab740550e993565f0f6.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/40/5014340a030a0d759a7ab740550e993565f0f6.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/38f210ab351af32e0720083f103d7c2164896c.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b8/38f210ab351af32e0720083f103d7c2164896c.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/b8/38f210ab351af32e0720083f103d7c2164896c.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: debian/samtools/usr/bin/md5fa contains an unresolvable reference to symbol __gnu_local_gp: it's probably a plugin
+dpkg-shlibdeps: warning: debian/samtools/usr/bin/md5sum-lite contains an unresolvable reference to symbol __gnu_local_gp: it's probably a plugin
+dpkg-shlibdeps: warning: debian/samtools/usr/bin/samtools contains an unresolvable reference to symbol __gnu_local_gp: it's probably a plugin
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools 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/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=0a2dd4fd75b72d0edd68257cee47205328502274 405014340a030a0d759a7ab740550e993565f0f6 60f48d480d541c8801acd3797905af36 [...]
+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 ${perl:Depends}
+ chmod 0644 debian/samtools/DEBIAN/control
+ chown 0:0 debian/samtools/DEBIAN/control
+ dh_md5sums -a -O--parallel
+ (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/samtools/DEBIAN/md5sums
+ chown 0:0 debian/samtools/DEBIAN/md5sums
+ (cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
+ dh_builddeb -a -O--parallel
+ dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_mipsel.deb'.
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mipsel-manda-02) <buildd_mipsel-mipsel-manda-02 at buildd.debian.org> >../samtools_1.3.1-1_mipsel.changes
+dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1730
+Build finished at 20160426-1308
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.3.1-1_mipsel.changes:
+────────────────────────────────
+
+Format: 1.8
+Date: Tue, 26 Apr 2016 21:12:05 +0900
+Source: samtools
+Binary: samtools samtools-test
+Architecture: mipsel
+Version: 1.3.1-1
+Distribution: sid
+Urgency: medium
+Maintainer: mipsel Build Daemon (mipsel-manda-02) <buildd_mipsel-mipsel-manda-02 at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package
+Changes:
+ samtools (1.3.1-1) unstable; urgency=medium
+ .
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
+Checksums-Sha1:
+ 5f284565dcc68c23626f104648898c6ceab0b407 462838 samtools-dbgsym_1.3.1-1_mipsel.deb
+ 79ab1d6723893cc639c843dc9eb85124fff84bac 239214 samtools_1.3.1-1_mipsel.deb
+Checksums-Sha256:
+ 4017facc6e85952670ffbfb10f0dbee81a1749026261843218606bcd8d031a2b 462838 samtools-dbgsym_1.3.1-1_mipsel.deb
+ 66da4e2411de86cdde683b59eaefc1a16c93496e5970540455c844678c3f4df4 239214 samtools_1.3.1-1_mipsel.deb
+Files:
+ 9b6bfddd9dc07a5ea57f725422f6a200 462838 debug extra samtools-dbgsym_1.3.1-1_mipsel.deb
+ 04497cc5419de5cc7f5d0ac2594d8e50 239214 science optional samtools_1.3.1-1_mipsel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools-dbgsym_1.3.1-1_mipsel.deb
+──────────────────────────────────
+
+ new debian package, version 2.0.
+ size 462838 bytes: control archive=821 bytes.
+ 651 bytes, 13 lines control
+ 742 bytes, 7 lines md5sums
+ Package: samtools-dbgsym
+ Source: samtools
+ Version: 1.3.1-1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 532
+ Depends: samtools (= 1.3.1-1)
+ Section: debug
+ Priority: extra
+ Homepage: http://www.htslib.org/
+ Description: Debug symbols for samtools
+ Auto-Built-Package: debug-symbols
+ Build-Ids: 0a2dd4fd75b72d0edd68257cee47205328502274 405014340a030a0d759a7ab740550e993565f0f6 60f48d480d541c8801acd3797905af369d782ce0 6984737eef6436818899c075426bcd61e2015378 b838f210ab351af32e0720083f103d7c2164896c c3afeeb9d0b56b65de341debe58d2f2f8e479820 fd5ced76163a2f5fed790513fdcd8bdb83bb87be
+
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/0a/
+-rw-r--r-- root/root 10680 2016-04-26 13:08 ./usr/lib/debug/.build-id/0a/2dd4fd75b72d0edd68257cee47205328502274.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/40/
+-rw-r--r-- root/root 18952 2016-04-26 13:08 ./usr/lib/debug/.build-id/40/5014340a030a0d759a7ab740550e993565f0f6.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/60/
+-rw-r--r-- root/root 19368 2016-04-26 13:08 ./usr/lib/debug/.build-id/60/f48d480d541c8801acd3797905af369d782ce0.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/69/
+-rw-r--r-- root/root 10844 2016-04-26 13:08 ./usr/lib/debug/.build-id/69/84737eef6436818899c075426bcd61e2015378.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/b8/
+-rw-r--r-- root/root 446580 2016-04-26 13:08 ./usr/lib/debug/.build-id/b8/38f210ab351af32e0720083f103d7c2164896c.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/c3/
+-rw-r--r-- root/root 10844 2016-04-26 13:08 ./usr/lib/debug/.build-id/c3/afeeb9d0b56b65de341debe58d2f2f8e479820.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/lib/debug/.build-id/fd/
+-rw-r--r-- root/root 7948 2016-04-26 13:08 ./usr/lib/debug/.build-id/fd/5ced76163a2f5fed790513fdcd8bdb83bb87be.debug
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 13:08 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_mipsel.deb
+───────────────────────────
+
+ new debian package, version 2.0.
+ size 239214 bytes: control archive=1637 bytes.
+ 809 bytes, 17 lines control
+ 1900 bytes, 32 lines md5sums
+ Package: samtools
+ Version: 1.3.1-1
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 740
+ 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 2016-04-26 13:08 ./
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/bin/
+-rwxr-xr-x root/root 18364 2016-04-26 13:08 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10192 2016-04-26 13:08 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10192 2016-04-26 13:08 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 10140 2016-04-26 13:08 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10072 2016-04-26 13:08 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 465388 2016-04-26 13:08 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22808 2016-04-26 13:08 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 13:08 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 13:08 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 13:08 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 13:08 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 13:08 ./usr/share/man/man1/wgsim.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1713,20 +2203,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mipsel
-Build-Space: 23920
-Build-Time: 401
+Build-Space: 21216
+Build-Time: 842
Distribution: sid
-Fail-Stage: build
Host Architecture: mipsel
-Install-Time: 69
-Job: samtools_1.3-1
+Install-Time: 62
+Job: samtools_1.3.1-1
Machine Architecture: mipsel
Package: samtools
-Package-Time: 565
-Source-Version: 1.3-1
-Space: 23920
-Status: attempted
-Version: 1.3-1
+Package-Time: 982
+Source-Version: 1.3.1-1
+Space: 21216
+Status: successful
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1730
-Build needed 00:09:25, 23920k disc space
+Finished at 20160426-1308
+Build needed 00:16:22, 21216k disc space
+Signature with key 'BE3B8D1C' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_mipsel.changes BE3B8D1C
+
+Successfully signed changes file
diff --git a/ppc64el.log b/ppc64el.log
index 0e9c674..903157f 100644
--- a/ppc64el.log
+++ b/ppc64el.log
@@ -1,45 +1,45 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on ppc64el-osuosl-01.debian.org
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on ppc64el-unicamp-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (ppc64el) 05 Feb 2016 16:33 ║
+║ samtools 1.3.1-1 (ppc64el) 26 Apr 2016 12:30 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: ppc64el
Host Architecture: ppc64el
Build Architecture: ppc64el
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-fXt_qD/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-fXt_qD' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-48fce04b-3af8-4044-8582-9a216e5c5ec6' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Get:1 http://ftp.br.debian.org/debian unstable InRelease [196 kB]
+Get:2 http://ftp.br.debian.org/debian unstable/main Sources [6767 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:4 http://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:5 http://ftp.br.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:6 http://ftp.br.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:7 http://ftp.br.debian.org/debian unstable/main ppc64el Packages [6853 kB]
+Get:8 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [102 kB]
+Get:9 http://ftp.br.debian.org/debian unstable/contrib ppc64el Packages [41.3 kB]
+Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [1004 B]
+Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/non-free Sources [32 B]
+Get:12 http://incoming.debian.org/debian-buildd buildd-unstable/main ppc64el Packages [122 kB]
+Get:13 http://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/contrib ppc64el Packages [2288 B]
+Get:15 http://ftp.debian.org/debian unstable/contrib Sources [48.6 kB]
+Get:16 http://ftp.debian.org/debian unstable/non-free Sources [84.1 kB]
+Get:17 http://ftp.debian.org/debian unstable/main ppc64el Packages [6853 kB]
+Get:18 http://ftp.debian.org/debian unstable/contrib ppc64el Packages [41.3 kB]
+Fetched 28.3 MB in 12s (2183 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -52,23 +52,22 @@ Check APT
─────────
Checking available source versions...
+W: apt-cache output for different version
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
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 1s (2100 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 7s (537 kB/s)
Download complete and in download only mode
Check architectures
@@ -82,16 +81,15 @@ 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-uhfl1o/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-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]
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-YQTZpk/apt_archive/sbuild-build-depends-core-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-YQTZpk/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-YQTZpk/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 +104,28 @@ 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 10 not upgraded.
-Need to get 0 B/772 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 31 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-uhfl1o/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
+Get:1 file:/«BUILDDIR»/resolver-YQTZpk/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 ... 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 ... 12166 files and directories currently installed.)
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
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(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12210 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 (>= 4:5.3), 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-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]
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-ZF4Jja/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Get:1 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Release.gpg
+Ign:3 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Release.gpg
+Get:4 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ Packages [743 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
@@ -142,79 +139,115 @@ 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool 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
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
Recommended packages:
- curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
- xml-core libmail-sendmail-perl
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev 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 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 1.22.3-7 [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 1.4.1-2 [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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 31 not upgraded.
+Need to get 25.0 MB/25.0 MB of archives.
+After this operation, 96.5 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-ZF4Jja/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [992 B]
+Get:2 http://ftp.br.debian.org/debian unstable/main ppc64el bash-completion all 1:2.1-4.3 [178 kB]
+Get:3 http://ftp.br.debian.org/debian unstable/main ppc64el groff-base ppc64el 1.22.3-7 [1229 kB]
+Get:4 http://ftp.br.debian.org/debian unstable/main ppc64el libbsd0 ppc64el 0.8.3-1 [82.7 kB]
+Get:5 http://ftp.br.debian.org/debian unstable/main ppc64el bsdmainutils ppc64el 9.0.10 [182 kB]
+Get:6 http://ftp.br.debian.org/debian unstable/main ppc64el libpipeline1 ppc64el 1.4.1-2 [26.6 kB]
+Get:7 http://ftp.br.debian.org/debian unstable/main ppc64el man-db ppc64el 2.7.5-1 [985 kB]
+Get:8 http://ftp.br.debian.org/debian unstable/main ppc64el autoconf-archive all 20150925-1 [688 kB]
+Get:9 http://ftp.br.debian.org/debian unstable/main ppc64el libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
+Get:10 http://ftp.br.debian.org/debian unstable/main ppc64el libssl1.0.2 ppc64el 1.0.2g-2 [964 kB]
+Get:11 http://ftp.br.debian.org/debian unstable/main ppc64el libmagic1 ppc64el 1:5.25-2 [253 kB]
+Get:12 http://ftp.br.debian.org/debian unstable/main ppc64el file ppc64el 1:5.25-2 [61.7 kB]
+Get:13 http://ftp.br.debian.org/debian unstable/main ppc64el gettext-base ppc64el 0.19.7-2 [113 kB]
+Get:14 http://ftp.br.debian.org/debian unstable/main ppc64el libnettle6 ppc64el 3.2-1 [207 kB]
+Get:15 http://ftp.br.debian.org/debian unstable/main ppc64el libhogweed4 ppc64el 3.2-1 [132 kB]
+Get:16 http://ftp.br.debian.org/debian unstable/main ppc64el libidn11 ppc64el 1.32-3 [112 kB]
+Get:17 http://ftp.br.debian.org/debian unstable/main ppc64el libffi6 ppc64el 3.2.1-4 [20.5 kB]
+Get:18 http://ftp.br.debian.org/debian unstable/main ppc64el libp11-kit0 ppc64el 0.23.2-3 [95.1 kB]
+Get:19 http://ftp.br.debian.org/debian unstable/main ppc64el libtasn1-6 ppc64el 4.8-1 [48.0 kB]
+Get:20 http://ftp.br.debian.org/debian unstable/main ppc64el libgnutls30 ppc64el 3.4.11-3 [700 kB]
+Get:21 http://ftp.br.debian.org/debian unstable/main ppc64el libkeyutils1 ppc64el 1.5.9-8 [12.0 kB]
+Get:22 http://ftp.br.debian.org/debian unstable/main ppc64el libkrb5support0 ppc64el 1.13.2+dfsg-5 [58.8 kB]
+Get:23 http://ftp.br.debian.org/debian unstable/main ppc64el libk5crypto3 ppc64el 1.13.2+dfsg-5 [117 kB]
+Get:24 http://ftp.br.debian.org/debian unstable/main ppc64el libkrb5-3 ppc64el 1.13.2+dfsg-5 [283 kB]
+Get:25 http://ftp.br.debian.org/debian unstable/main ppc64el libgssapi-krb5-2 ppc64el 1.13.2+dfsg-5 [140 kB]
+Get:26 http://ftp.br.debian.org/debian unstable/main ppc64el libsasl2-modules-db ppc64el 2.1.26.dfsg1-15 [66.6 kB]
+Get:27 http://ftp.br.debian.org/debian unstable/main ppc64el libsasl2-2 ppc64el 2.1.26.dfsg1-15 [100 kB]
+Get:28 http://ftp.br.debian.org/debian unstable/main ppc64el libldap-2.4-2 ppc64el 2.4.42+dfsg-2+b2 [208 kB]
+Get:29 http://ftp.br.debian.org/debian unstable/main ppc64el libicu55 ppc64el 55.1-7 [7626 kB]
+Get:30 http://ftp.br.debian.org/debian unstable/main ppc64el libxml2 ppc64el 2.9.3+dfsg1-1 [830 kB]
+Get:31 http://ftp.br.debian.org/debian unstable/main ppc64el libsigsegv2 ppc64el 2.10-5 [28.8 kB]
+Get:32 http://ftp.br.debian.org/debian unstable/main ppc64el m4 ppc64el 1.4.17-5 [248 kB]
+Get:33 http://ftp.br.debian.org/debian unstable/main ppc64el autoconf all 2.69-10 [338 kB]
+Get:34 http://ftp.br.debian.org/debian unstable/main ppc64el autotools-dev all 20150820.1 [71.7 kB]
+Get:35 http://ftp.br.debian.org/debian unstable/main ppc64el automake all 1:1.15-4 [735 kB]
+Get:36 http://ftp.br.debian.org/debian unstable/main ppc64el autopoint all 0.19.7-2 [424 kB]
+Get:37 http://ftp.br.debian.org/debian unstable/main ppc64el libglib2.0-0 ppc64el 2.48.0-1 [2561 kB]
+Get:38 http://ftp.br.debian.org/debian unstable/main ppc64el libcroco3 ppc64el 0.6.11-1 [133 kB]
+Get:39 http://ftp.br.debian.org/debian unstable/main ppc64el gettext ppc64el 0.19.7-2 [1430 kB]
+Get:40 http://ftp.br.debian.org/debian unstable/main ppc64el intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:41 http://ftp.br.debian.org/debian unstable/main ppc64el po-debconf all 1.0.19 [249 kB]
+Get:42 http://ftp.br.debian.org/debian unstable/main ppc64el libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:43 http://ftp.br.debian.org/debian unstable/main ppc64el libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:44 http://ftp.br.debian.org/debian unstable/main ppc64el libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:45 http://ftp.br.debian.org/debian unstable/main ppc64el dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:46 http://ftp.br.debian.org/debian unstable/main ppc64el libtool all 2.4.6-0.1 [200 kB]
+Get:47 http://ftp.br.debian.org/debian unstable/main ppc64el dh-autoreconf all 12 [15.8 kB]
+Get:48 http://ftp.br.debian.org/debian unstable/main ppc64el debhelper all 9.20160403 [800 kB]
+Get:49 http://ftp.br.debian.org/debian unstable/main ppc64el libnghttp2-14 ppc64el 1.9.2-1 [71.4 kB]
+Get:50 http://ftp.br.debian.org/debian unstable/main ppc64el librtmp1 ppc64el 2.4+20151223.gitfa8646d-1+b1 [56.8 kB]
+Get:51 http://ftp.br.debian.org/debian unstable/main ppc64el libssh2-1 ppc64el 1.5.0-2.1 [128 kB]
+Get:52 http://ftp.br.debian.org/debian unstable/main ppc64el libcurl3-gnutls ppc64el 7.47.0-1 [254 kB]
+Get:53 http://ftp.br.debian.org/debian unstable/main ppc64el libhts1 ppc64el 1.3.1-1 [237 kB]
+Get:54 http://ftp.br.debian.org/debian unstable/main ppc64el libhts-dev ppc64el 1.3.1-1 [308 kB]
+Get:55 http://ftp.br.debian.org/debian unstable/main ppc64el libio-pty-perl ppc64el 1:1.08-1.1+b1 [33.0 kB]
+Get:56 http://ftp.br.debian.org/debian unstable/main ppc64el libtinfo-dev ppc64el 6.0+20160319-1 [77.7 kB]
+Get:57 http://ftp.br.debian.org/debian unstable/main ppc64el libncurses5-dev ppc64el 6.0+20160319-1 [175 kB]
+Get:58 http://ftp.br.debian.org/debian unstable/main ppc64el tabix ppc64el 1.3.1-1 [227 kB]
+Get:59 http://ftp.br.debian.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 20.4 MB in 1s (16.3 MB/s)
+Fetched 25.0 MB in 2s (10.6 MB/s)
Selecting previously unselected package bash-completion.
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-Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
-Unpacking bash-completion (1:2.1-4.2) ...
+(Reading database ...
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(Reading database ... 12210 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_ppc64el.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:ppc64el.
+Preparing to unpack .../libbsd0_0.8.3-1_ppc64el.deb ...
+Unpacking libbsd0:ppc64el (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_ppc64el.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_ppc64el.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:ppc64el.
Preparing to unpack .../libpipeline1_1.4.1-2_ppc64el.deb ...
Unpacking libpipeline1:ppc64el (1.4.1-2) ...
@@ -224,12 +257,12 @@ 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.
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-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) ...
+Selecting previously unselected package libssl1.0.2:ppc64el.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_ppc64el.deb ...
+Unpacking libssl1.0.2:ppc64el (1.0.2g-2) ...
Selecting previously unselected package libmagic1:ppc64el.
Preparing to unpack .../libmagic1_1%3a5.25-2_ppc64el.deb ...
Unpacking libmagic1:ppc64el (1:5.25-2) ...
@@ -239,30 +272,78 @@ Unpacking file (1:5.25-2) ...
Selecting previously unselected package gettext-base.
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Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:ppc64el.
+Preparing to unpack .../libnettle6_3.2-1_ppc64el.deb ...
+Unpacking libnettle6:ppc64el (3.2-1) ...
+Selecting previously unselected package libhogweed4:ppc64el.
+Preparing to unpack .../libhogweed4_3.2-1_ppc64el.deb ...
+Unpacking libhogweed4:ppc64el (3.2-1) ...
+Selecting previously unselected package libidn11:ppc64el.
+Preparing to unpack .../libidn11_1.32-3_ppc64el.deb ...
+Unpacking libidn11:ppc64el (1.32-3) ...
+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 libp11-kit0:ppc64el.
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+Unpacking libp11-kit0:ppc64el (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:ppc64el.
+Preparing to unpack .../libtasn1-6_4.8-1_ppc64el.deb ...
+Unpacking libtasn1-6:ppc64el (4.8-1) ...
+Selecting previously unselected package libgnutls30:ppc64el.
+Preparing to unpack .../libgnutls30_3.4.11-3_ppc64el.deb ...
+Unpacking libgnutls30:ppc64el (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:ppc64el.
+Preparing to unpack .../libkeyutils1_1.5.9-8_ppc64el.deb ...
+Unpacking libkeyutils1:ppc64el (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:ppc64el.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_ppc64el.deb ...
+Unpacking libkrb5support0:ppc64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:ppc64el.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_ppc64el.deb ...
+Unpacking libk5crypto3:ppc64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:ppc64el.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_ppc64el.deb ...
+Unpacking libkrb5-3:ppc64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:ppc64el.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_ppc64el.deb ...
+Unpacking libgssapi-krb5-2:ppc64el (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:ppc64el.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_ppc64el.deb ...
+Unpacking libsasl2-modules-db:ppc64el (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:ppc64el.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_ppc64el.deb ...
+Unpacking libsasl2-2:ppc64el (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:ppc64el.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_ppc64el.deb ...
+Unpacking libldap-2.4-2:ppc64el (2.4.42+dfsg-2+b2) ...
Selecting previously unselected package libicu55:ppc64el.
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Unpacking libicu55:ppc64el (55.1-7) ...
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Unpacking libxml2:ppc64el (2.9.3+dfsg1-1) ...
+Selecting previously unselected package libsigsegv2:ppc64el.
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+Unpacking libsigsegv2:ppc64el (2.10-5) ...
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Unpacking m4 (1.4.17-5) ...
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Unpacking autotools-dev (20150820.1) ...
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-Unpacking libffi6:ppc64el (3.2.1-4) ...
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+Unpacking automake (1:1.15-4) ...
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+Unpacking autopoint (0.19.7-2) ...
Selecting previously unselected package libglib2.0-0:ppc64el.
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-Unpacking libglib2.0-0:ppc64el (2.46.2-3) ...
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+Unpacking libglib2.0-0:ppc64el (2.48.0-1) ...
Selecting previously unselected package libcroco3:ppc64el.
Preparing to unpack .../libcroco3_0.6.11-1_ppc64el.deb ...
Unpacking libcroco3:ppc64el (0.6.11-1) ...
@@ -276,87 +357,128 @@ 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.
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-Unpacking libarchive-zip-perl (1.56-2) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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-Unpacking libfile-stripnondeterminism-perl (0.015-1) ...
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+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
Selecting previously unselected package libtimedate-perl.
Preparing to unpack .../libtimedate-perl_2.3000-2_all.deb ...
Unpacking libtimedate-perl (2.3000-2) ...
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-Unpacking dh-strip-nondeterminism (0.015-1) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
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-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:ppc64el.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_ppc64el.deb ...
+Unpacking libnghttp2-14:ppc64el (1.9.2-1) ...
+Selecting previously unselected package librtmp1:ppc64el.
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+Unpacking librtmp1:ppc64el (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:ppc64el.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_ppc64el.deb ...
+Unpacking libssh2-1:ppc64el (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:ppc64el.
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+Unpacking libcurl3-gnutls:ppc64el (7.47.0-1) ...
Selecting previously unselected package libhts1:ppc64el.
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+Unpacking libhts1:ppc64el (1.3.1-1) ...
Selecting previously unselected package libhts-dev:ppc64el.
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-Unpacking libhts-dev:ppc64el (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_ppc64el.deb ...
+Unpacking libhts-dev:ppc64el (1.3.1-1) ...
Selecting previously unselected package libio-pty-perl.
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Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:ppc64el.
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-Unpacking libtinfo-dev:ppc64el (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_ppc64el.deb ...
+Unpacking libtinfo-dev:ppc64el (6.0+20160319-1) ...
Selecting previously unselected package libncurses5-dev:ppc64el.
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-Unpacking libncurses5-dev:ppc64el (6.0+20151024-2) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_ppc64el.deb ...
+Unpacking libncurses5-dev:ppc64el (6.0+20160319-1) ...
Selecting previously unselected package tabix.
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-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../tabix_1.3.1-1_ppc64el.deb ...
+Unpacking tabix (1.3.1-1) ...
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.
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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) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:ppc64el (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 (1.4.1-2) ...
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 libssl1.0.2:ppc64el (1.0.2g-2) ...
Setting up libmagic1:ppc64el (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:ppc64el (3.2-1) ...
+Setting up libhogweed4:ppc64el (3.2-1) ...
+Setting up libidn11:ppc64el (1.32-3) ...
+Setting up libffi6:ppc64el (3.2.1-4) ...
+Setting up libp11-kit0:ppc64el (0.23.2-3) ...
+Setting up libtasn1-6:ppc64el (4.8-1) ...
+Setting up libgnutls30:ppc64el (3.4.11-3) ...
+Setting up libkeyutils1:ppc64el (1.5.9-8) ...
+Setting up libkrb5support0:ppc64el (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:ppc64el (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:ppc64el (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:ppc64el (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:ppc64el (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:ppc64el (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:ppc64el (2.4.42+dfsg-2+b2) ...
Setting up libicu55:ppc64el (55.1-7) ...
Setting up libxml2:ppc64el (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:ppc64el (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
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 (2.46.2-3) ...
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:ppc64el (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:ppc64el (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:ppc64el (1.3-1) ...
-Setting up libhts-dev:ppc64el (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:ppc64el (1.9.2-1) ...
+Setting up librtmp1:ppc64el (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:ppc64el (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:ppc64el (7.47.0-1) ...
+Setting up libhts1:ppc64el (1.3.1-1) ...
+Setting up libhts-dev:ppc64el (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:ppc64el (6.0+20160319-1) ...
+Setting up libncurses5-dev:ppc64el (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -364,8 +486,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -376,12 +498,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -394,7 +516,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=4
+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
@@ -403,23 +525,23 @@ SCHROOT_CHROOT_NAME=sid-ppc64el-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ppc64el-sbuild-86091641-d380-44ba-8303-2e9b0d56163f
+SCHROOT_SESSION_ID=sid-ppc64el-sbuild-48fce04b-3af8-4044-8582-9a216e5c5ec6
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/2952
-XDG_SESSION_ID=2
+XDG_SESSION_ID=6
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture ppc64el
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -427,7 +549,7 @@ dh clean --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
touch config.mk
dh_auto_clean --
- make -j4 distclean
+ 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
@@ -466,15 +588,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -486,6 +608,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -504,84 +628,84 @@ 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 -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 -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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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/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_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»'
@@ -589,40 +713,40 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
- make -j4 test BGZIP=/usr/bin/bgzip
+ make -j8 test VERBOSE=1 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/_Ps6Q96Nl9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/21BZ1T4I3z/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/_Ps6Q96Nl9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/21BZ1T4I3z/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/_Ps6Q96Nl9/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/21BZ1T4I3z/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/_Ps6Q96Nl9/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/21BZ1T4I3z/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
@@ -630,7 +754,7 @@ test_dict:
.. ok
test_dict:
- /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/_Ps6Q96Nl9/dict.fa.gz
+ /«PKGBUILDDIR»/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/21BZ1T4I3z/dict.fa.gz
.. ok
test_dict:
@@ -638,17 +762,17 @@ test_dict:
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/_Ps6Q96Nl9/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/21BZ1T4I3z/large_chrom.bam
ERR:
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/_Ps6Q96Nl9/large_chrom.bam ref2
+ /«PKGBUILDDIR»/samtools view /tmp/21BZ1T4I3z/large_chrom.bam ref2
.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/_Ps6Q96Nl9/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/21BZ1T4I3z/large_chrom.bam ref2:1-541556283
.. ok
test_index:
@@ -656,35 +780,35 @@ test_index:
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/_Ps6Q96Nl9/mpileup.bam.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/21BZ1T4I3z/mpileup.bam.list -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/21BZ1T4I3z/mpileup.cram.list -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/21BZ1T4I3z/mpileup.bam.list -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«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
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/21BZ1T4I3z/mpileup.cram.list -f /tmp/21BZ1T4I3z/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/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/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/21BZ1T4I3z/mpileup.cram.list -f /tmp/21BZ1T4I3z/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/_Ps6Q96Nl9/mpileup.cram.list -f /tmp/_Ps6Q96Nl9/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/21BZ1T4I3z/mpileup.cram.list -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:1050-1060 /tmp/21BZ1T4I3z/mpileup.1.bam | grep -v mpileup
.. ok
test_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
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/21BZ1T4I3z/mpileup.ref.fa.gz -r17:1050-1060 /tmp/21BZ1T4I3z/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
@@ -934,41 +1058,41 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/21BZ1T4I3z/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/21BZ1T4I3z/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/21BZ1T4I3z/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/21BZ1T4I3z/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/21BZ1T4I3z/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/21BZ1T4I3z/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/_Ps6Q96Nl9/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/21BZ1T4I3z/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/_Ps6Q96Nl9/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/21BZ1T4I3z/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
@@ -982,419 +1106,431 @@ test_view:
72: Count -l Library 2 (CRAM input) .. ok
- 73: Filter -q 50 (SAM input) .. ok
+ 73: Filter -l Library 3 (SAM input) .. ok
- 74: Count -q 50 (SAM input) .. ok
+ 74: Count -l Library 3 (SAM input) .. ok
- 75: Filter -q 50 (BAM input) .. ok
+ 75: Filter -l Library 3 (BAM input) .. ok
- 76: Count -q 50 (BAM input) .. ok
+ 76: Count -l Library 3 (BAM input) .. ok
- 77: Filter -q 50 (CRAM input) .. ok
+ 77: Filter -l Library 3 (CRAM input) .. ok
- 78: Count -q 50 (CRAM input) .. ok
+ 78: Count -l Library 3 (CRAM input) .. ok
- 79: Filter -q 99 (SAM input) .. ok
+ 79: Filter -q 50 (SAM input) .. ok
- 80: Count -q 99 (SAM input) .. ok
+ 80: Count -q 50 (SAM input) .. ok
- 81: Filter -q 99 (BAM input) .. ok
+ 81: Filter -q 50 (BAM input) .. ok
- 82: Count -q 99 (BAM input) .. ok
+ 82: Count -q 50 (BAM input) .. ok
- 83: Filter -q 99 (CRAM input) .. ok
+ 83: Filter -q 50 (CRAM input) .. ok
- 84: Count -q 99 (CRAM input) .. ok
+ 84: Count -q 50 (CRAM input) .. ok
- 85: Filter -q 100 (SAM input) .. ok
+ 85: Filter -q 99 (SAM input) .. ok
- 86: Count -q 100 (SAM input) .. ok
+ 86: Count -q 99 (SAM input) .. ok
- 87: Filter -q 100 (BAM input) .. ok
+ 87: Filter -q 99 (BAM input) .. ok
- 88: Count -q 100 (BAM input) .. ok
+ 88: Count -q 99 (BAM input) .. ok
- 89: Filter -q 100 (CRAM input) .. ok
+ 89: Filter -q 99 (CRAM input) .. ok
- 90: Count -q 100 (CRAM input) .. ok
+ 90: Count -q 99 (CRAM input) .. ok
- 91: Filter -x fa (SAM input) .. ok
+ 91: Filter -q 100 (SAM input) .. ok
- 92: Count -x fa (SAM input) .. ok
+ 92: Count -q 100 (SAM input) .. ok
- 93: Filter -x fa (BAM input) .. ok
+ 93: Filter -q 100 (BAM input) .. ok
- 94: Count -x fa (BAM input) .. ok
+ 94: Count -q 100 (BAM input) .. ok
- 95: Filter -x fa (CRAM input) .. ok
+ 95: Filter -q 100 (CRAM input) .. ok
- 96: Count -x fa (CRAM input) .. ok
+ 96: Count -q 100 (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input) .. ok
+ 97: Filter -x fa (SAM input) .. ok
- 98: Count -x fa -x ha (SAM input) .. ok
+ 98: Count -x fa (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input) .. ok
+ 99: Filter -x fa (BAM input) .. ok
- 100: Count -x fa -x ha (BAM input) .. ok
+ 100: Count -x fa (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input) .. ok
+ 101: Filter -x fa (CRAM input) .. ok
- 102: Count -x fa -x ha (CRAM input) .. ok
+ 102: Count -x fa (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input) .. ok
+ 103: Filter -x fa -x ha (SAM input) .. ok
- 104: Count -x fa -r grp2 (SAM input) .. ok
+ 104: Count -x fa -x ha (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input) .. ok
+ 105: Filter -x fa -x ha (BAM input) .. ok
- 106: Count -x fa -r grp2 (BAM input) .. ok
+ 106: Count -x fa -x ha (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
+ 107: Filter -x fa -x ha (CRAM input) .. ok
- 108: Count -x fa -r grp2 (CRAM input) .. ok
+ 108: Count -x fa -x ha (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input) .. ok
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
- 110: Count -x RG -r grp2 (SAM input) .. ok
+ 110: Count -x fa -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input) .. ok
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
- 112: Count -x RG -r grp2 (BAM input) .. ok
+ 112: Count -x fa -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
- 114: Count -x RG -r grp2 (CRAM input) .. ok
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input) .. ok
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
- 116: Count -m 10 (SAM input) .. ok
+ 116: Count -x RG -r grp2 (SAM input) .. ok
- 117: Filter -m 10 (BAM input) .. ok
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
- 118: Count -m 10 (BAM input) .. ok
+ 118: Count -x RG -r grp2 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input) .. ok
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
- 120: Count -m 10 (CRAM input) .. ok
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
- 121: Filter -m 11 (SAM input) .. ok
+ 121: Filter -m 10 (SAM input) .. ok
- 122: Count -m 11 (SAM input) .. ok
+ 122: Count -m 10 (SAM input) .. ok
- 123: Filter -m 11 (BAM input) .. ok
+ 123: Filter -m 10 (BAM input) .. ok
- 124: Count -m 11 (BAM input) .. ok
+ 124: Count -m 10 (BAM input) .. ok
- 125: Filter -m 11 (CRAM input) .. ok
+ 125: Filter -m 10 (CRAM input) .. ok
- 126: Count -m 11 (CRAM input) .. ok
+ 126: Count -m 10 (CRAM input) .. ok
- 127: Filter -m 15 (SAM input) .. ok
+ 127: Filter -m 11 (SAM input) .. ok
- 128: Count -m 15 (SAM input) .. ok
+ 128: Count -m 11 (SAM input) .. ok
- 129: Filter -m 15 (BAM input) .. ok
+ 129: Filter -m 11 (BAM input) .. ok
- 130: Count -m 15 (BAM input) .. ok
+ 130: Count -m 11 (BAM input) .. ok
- 131: Filter -m 15 (CRAM input) .. ok
+ 131: Filter -m 11 (CRAM input) .. ok
- 132: Count -m 15 (CRAM input) .. ok
+ 132: Count -m 11 (CRAM input) .. ok
- 133: Filter -m 16 (SAM input) .. ok
+ 133: Filter -m 15 (SAM input) .. ok
- 134: Count -m 16 (SAM input) .. ok
+ 134: Count -m 15 (SAM input) .. ok
- 135: Filter -m 16 (BAM input) .. ok
+ 135: Filter -m 15 (BAM input) .. ok
- 136: Count -m 16 (BAM input) .. ok
+ 136: Count -m 15 (BAM input) .. ok
- 137: Filter -m 16 (CRAM input) .. ok
+ 137: Filter -m 15 (CRAM input) .. ok
- 138: Count -m 16 (CRAM input) .. ok
+ 138: Count -m 15 (CRAM input) .. ok
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
+ 139: Filter -m 16 (SAM input) .. ok
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+ 140: Count -m 16 (SAM input) .. ok
- 140: Region Z (BAM input) .. ok
+ 141: Filter -m 16 (BAM input) .. ok
- 141: Count Z (BAM input) .. ok
+ 142: Count -m 16 (BAM input) .. ok
- 142: Region Z (CRAM input) .. ok
+ 143: Filter -m 16 (CRAM input) .. ok
- 143: Count Z (CRAM input) .. ok
+ 144: Count -m 16 (CRAM input) .. ok
- 144: Region Z:30 (BAM input) .. ok
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
- 145: Count Z:30 (BAM input) .. ok
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
- 146: Region Z:30 (CRAM input) .. ok
+ 146: Region Z (BAM input) .. ok
- 147: Count Z:30 (CRAM input) .. ok
+ 147: Count Z (BAM input) .. ok
- 148: Region Z:20-40 (BAM input) .. ok
+ 148: Region Z (CRAM input) .. ok
- 149: Count Z:20-40 (BAM input) .. ok
+ 149: Count Z (CRAM input) .. ok
- 150: Region Z:20-40 (CRAM input) .. ok
+ 150: Region Z:30 (BAM input) .. ok
- 151: Count Z:20-40 (CRAM input) .. ok
+ 151: Count Z:30 (BAM input) .. ok
- 152: Region ref1 (BAM input) .. ok
+ 152: Region Z:30 (CRAM input) .. ok
- 153: Count ref1 (BAM input) .. ok
+ 153: Count Z:30 (CRAM input) .. ok
- 154: Region ref1 (CRAM input) .. ok
+ 154: Region Z:20-40 (BAM input) .. ok
- 155: Count ref1 (CRAM input) .. ok
+ 155: Count Z:20-40 (BAM input) .. ok
- 156: Region ref1:15 (BAM input) .. ok
+ 156: Region Z:20-40 (CRAM input) .. ok
- 157: Count ref1:15 (BAM input) .. ok
+ 157: Count Z:20-40 (CRAM input) .. ok
- 158: Region ref1:15 (CRAM input) .. ok
+ 158: Region ref1 (BAM input) .. ok
- 159: Count ref1:15 (CRAM input) .. ok
+ 159: Count ref1 (BAM input) .. ok
- 160: Region ref1:15-45 (BAM input) .. ok
+ 160: Region ref1 (CRAM input) .. ok
- 161: Count ref1:15-45 (BAM input) .. ok
+ 161: Count ref1 (CRAM input) .. ok
- 162: Region ref1:15-45 (CRAM input) .. ok
+ 162: Region ref1:15 (BAM input) .. ok
- 163: Count ref1:15-45 (CRAM input) .. ok
+ 163: Count ref1:15 (BAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
+ 164: Region ref1:15 (CRAM input) .. ok
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
+ 165: Count ref1:15 (CRAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+ 166: Region ref1:15-45 (BAM input) .. ok
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+ 167: Count ref1:15-45 (BAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+ 168: Region ref1:15-45 (CRAM input) .. ok
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+ 169: Count ref1:15-45 (CRAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 180: Region -f 128 ref1 (BAM input) .. ok
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 181: Count -f 128 ref1 (BAM input) .. ok
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 182: Region -f 128 ref1 (CRAM input) .. ok
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
- 183: Count -f 128 ref1 (CRAM input) .. ok
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+ 186: Region -f 128 ref1 (BAM input) .. ok
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+ 187: Count -f 128 ref1 (BAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+ 188: Region -f 128 ref1 (CRAM input) .. ok
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+ 189: Count -f 128 ref1 (CRAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
- 192: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
- 193: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 194: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
- 195: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 196: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
- 197: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
- 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 201: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 203: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 205: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
- 208: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 209: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
- 210: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 211: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
- 212: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 213: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
- 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
- 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
- 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
- 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
- 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
- 224: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 225: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 227: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
- 228: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 229: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
- 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
- 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
- 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
- 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
- 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
- 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
- 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
- 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
- 248: Make BAM with no M5/UR tags .. ok
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
- 250: Add @SQ with -T (SAM -> SAM) .. ok
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 251: Add @SQ with -t (BAM -> SAM) .. ok
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
- 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 253: Add @SQ with -t (SAM -> BAM) .. ok
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
- 254: Add @SQ with -T (SAM -> BAM) .. ok
+ 254: Make BAM with no M5/UR tags .. ok
- 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
- 261: Make CRAM with no UR field .. ok
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
- 262: Decoding CRAM with no UR field via -T .. ok
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
- 263: CIGAR B-operator removal .. ok
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
- 264: Big SAM -> BAM .. ok
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
- 265: Big SAM -> BAM (2 threads) .. ok
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
- 266: Big SAM -> BAM (4 threads) .. ok
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
- 267: Big SAM -> CRAM .. ok
+ 267: Make CRAM with no UR field .. ok
- 268: Big SAM -> CRAM (2 threads) .. ok
+ 268: Decoding CRAM with no UR field via -T .. ok
- 269: Big SAM -> CRAM (4 threads) .. ok
+ 269: CIGAR B-operator removal .. ok
- 270: Subsample 0.2 (SAM input) ............ ok
+ 270: Big SAM -> BAM .. ok
- 271: Subsample 0.5 (SAM input) ............ ok
+ 271: Big SAM -> BAM (2 threads) .. ok
- 272: Subsample 0.8 (SAM input) ............ ok
+ 272: Big SAM -> BAM (4 threads) .. ok
- 273: Subsample 0.2 (BAM input) ............ ok
+ 273: Big SAM -> CRAM .. ok
- 274: Subsample 0.5 (BAM input) ............ ok
+ 274: Big SAM -> CRAM (2 threads) .. ok
- 275: Subsample 0.8 (BAM input) ............ ok
+ 275: Big SAM -> CRAM (4 threads) .. ok
- 276: Subsample 0.2 (CRAM input) ............ ok
+ 276: Subsample 0.2 (SAM input) ............ ok
- 277: Subsample 0.5 (CRAM input) ............ ok
+ 277: Subsample 0.5 (SAM input) ............ ok
- 278: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (SAM input) ............ ok
+
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1542,7 +1678,7 @@ test_merge:
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/3akp4iF0QF - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/JGwfznIQX8 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_merge:
@@ -1562,15 +1698,15 @@ test_merge:
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sortout
+ /«PKGBUILDDIR»/samtools sort /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/21BZ1T4I3z/sortout
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sortout.bam
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/21BZ1T4I3z/sortout.bam
.. ok
test_sort:
- /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/_Ps6Q96Nl9/sorttmp
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/21BZ1T4I3z/sorttmp
.. ok
test_fixmate:
@@ -1624,8 +1760,18 @@ test_quickcheck:
.. 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
+ /«PKGBUILDDIR»/samtools quickcheck /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
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:.*//'
@@ -1673,10 +1819,10 @@ test_addrprg:
Number of tests:
- total .. 416
- passed .. 398
+ total .. 423
+ passed .. 403
failed .. 0
- expected failure .. 18
+ expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1686,12 +1832,9 @@ 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}'
-
-Expected passes: 123
+Expected passes: 124
Unexpected passes: 0
-Expected failures: 1
+Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
@@ -1721,7 +1864,7 @@ 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 -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
@@ -1773,7 +1916,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -1796,41 +1939,41 @@ 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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a/81dc0caab1c1be8c06c8bb06b9e2b98d55fed8.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a/81dc0caab1c1be8c06c8bb06b9e2b98d55fed8.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0a/81dc0caab1c1be8c06c8bb06b9e2b98d55fed8.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/72891375e9dce310c9f4736b7e70d78cc74ffa.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/72891375e9dce310c9f4736b7e70d78cc74ffa.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/20/72891375e9dce310c9f4736b7e70d78cc74ffa.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/570ab4556906a4c6b9f473e11a6b708e0b5cb9.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/570ab4556906a4c6b9f473e11a6b708e0b5cb9.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/7e/570ab4556906a4c6b9f473e11a6b708e0b5cb9.debug debian/samtools/usr/bin/md5fa
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/052ff7cf3b951d96c587fed825822a83fa0074.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/052ff7cf3b951d96c587fed825822a83fa0074.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/02/052ff7cf3b951d96c587fed825822a83fa0074.debug debian/samtools/usr/bin/maq2sam-short
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4/d2a46f8ef709b4dd3e1e49c5f88262d1e4b788.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4/d2a46f8ef709b4dd3e1e49c5f88262d1e4b788.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d4/d2a46f8ef709b4dd3e1e49c5f88262d1e4b788.debug debian/samtools/usr/bin/maq2sam-long
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/4e6b4d6c2ce593bcf273aa0e5cfb6305209322.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/4e6b4d6c2ce593bcf273aa0e5cfb6305209322.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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/08/4e6b4d6c2ce593bcf273aa0e5cfb6305209322.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c/62cecb377a7c5a369a49b8373862ec6aebafa8.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c/62cecb377a7c5a369a49b8373862ec6aebafa8.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/2a/5318e9ca372729356fe0d64b913ecbe0431430.debug debian/samtools/usr/bin/samtools
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/8c/62cecb377a7c5a369a49b8373862ec6aebafa8.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
@@ -1838,13 +1981,13 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5fa 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/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 -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=02052ff7cf3b951d96c587fed825822a83fa0074 084e6b4d6c2ce593bcf273aa0e5cfb6305209322 0a81dc0caab1c1be8c06c8bb06b9e2b9 [...]
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
@@ -1863,17 +2006,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_ppc64el.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_ppc64el.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_ppc64el.deb'.
- dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org> >../samtools_1.3-1_ppc64el.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_ppc64el.deb'.
+ dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-unicamp-01) <buildd_ppc64el-ppc64el-unicamp-01 at buildd.debian.org> >../samtools_1.3.1-1_ppc64el.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1637
+Build finished at 20160426-1233
Finished
────────
@@ -1890,108 +2033,100 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_ppc64el.changes:
-───────────────────────────────
+samtools_1.3.1-1_ppc64el.changes:
+─────────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: ppc64el
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: ppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: ppc64el Build Daemon (ppc64el-unicamp-01) <buildd_ppc64el-ppc64el-unicamp-01 at buildd.debian.org>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 3c3bed70b78b5fb18dca99a58ca4e0b495ae4561 468400 samtools-dbgsym_1.3-1_ppc64el.deb
- eea1683836476a760df4ce3e89033479c0b4e449 236130 samtools_1.3-1_ppc64el.deb
+ df62c2e9b8c667194f295c0eb74ac8a7f21bac86 477374 samtools-dbgsym_1.3.1-1_ppc64el.deb
+ 4be720059975e0b4ed69ab9f204cc625b9daed26 240616 samtools_1.3.1-1_ppc64el.deb
Checksums-Sha256:
- 5693b6d49d791bb301920185fd012a5b5aa890183e39daec8f6227a196457b9e 468400 samtools-dbgsym_1.3-1_ppc64el.deb
- 56f69eb5e72679faf47b78c45ad0ed7388125b73ccdd51bf147676fc5425fce4 236130 samtools_1.3-1_ppc64el.deb
+ 24568e1c928a1b08491ac2f37945582d7a591139062ccc96c9886a8e2686c0ea 477374 samtools-dbgsym_1.3.1-1_ppc64el.deb
+ c0f6612692ea868f33ac95e596eb344f8bb255b94507a2e987f34b4dbe6f8408 240616 samtools_1.3.1-1_ppc64el.deb
Files:
- 8e3ede7703e572b997654e0dbacca25f 468400 debug extra samtools-dbgsym_1.3-1_ppc64el.deb
- 25b1b9f46928562ddad7fa59f9c459b9 236130 science optional samtools_1.3-1_ppc64el.deb
+ da10cbf3b3b3eb8b6746071ff541a965 477374 debug extra samtools-dbgsym_1.3.1-1_ppc64el.deb
+ 1885fffafcbecab05b59f2e4fda54c4e 240616 science optional samtools_1.3.1-1_ppc64el.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_ppc64el.deb
-─────────────────────────────────
+samtools-dbgsym_1.3.1-1_ppc64el.deb
+───────────────────────────────────
new debian package, version 2.0.
- size 468400 bytes: control archive=819 bytes.
- 648 bytes, 13 lines control
+ size 477374 bytes: control archive=818 bytes.
+ 652 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: ppc64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 553
- Depends: samtools (= 1.3-1)
+ Installed-Size: 562
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- 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
-──────────────────────────
+ Build-Ids: 02052ff7cf3b951d96c587fed825822a83fa0074 084e6b4d6c2ce593bcf273aa0e5cfb6305209322 0a81dc0caab1c1be8c06c8bb06b9e2b98d55fed8 2072891375e9dce310c9f4736b7e70d78cc74ffa 7e570ab4556906a4c6b9f473e11a6b708e0b5cb9 8c62cecb377a7c5a369a49b8373862ec6aebafa8 d4d2a46f8ef709b4dd3e1e49c5f88262d1e4b788
+
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/02/
+-rw-r--r-- root/root 13040 2016-04-26 12:33 ./usr/lib/debug/.build-id/02/052ff7cf3b951d96c587fed825822a83fa0074.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/08/
+-rw-r--r-- root/root 21440 2016-04-26 12:33 ./usr/lib/debug/.build-id/08/4e6b4d6c2ce593bcf273aa0e5cfb6305209322.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/0a/
+-rw-r--r-- root/root 21824 2016-04-26 12:33 ./usr/lib/debug/.build-id/0a/81dc0caab1c1be8c06c8bb06b9e2b98d55fed8.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/20/
+-rw-r--r-- root/root 9624 2016-04-26 12:33 ./usr/lib/debug/.build-id/20/72891375e9dce310c9f4736b7e70d78cc74ffa.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/7e/
+-rw-r--r-- root/root 12848 2016-04-26 12:33 ./usr/lib/debug/.build-id/7e/570ab4556906a4c6b9f473e11a6b708e0b5cb9.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/8c/
+-rw-r--r-- root/root 464632 2016-04-26 12:33 ./usr/lib/debug/.build-id/8c/62cecb377a7c5a369a49b8373862ec6aebafa8.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/lib/debug/.build-id/d4/
+-rw-r--r-- root/root 13016 2016-04-26 12:33 ./usr/lib/debug/.build-id/d4/d2a46f8ef709b4dd3e1e49c5f88262d1e4b788.debug
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 12:33 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_ppc64el.deb
+────────────────────────────
new debian package, version 2.0.
- size 236130 bytes: control archive=1634 bytes.
+ size 240616 bytes: control archive=1636 bytes.
810 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: ppc64el
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1060
- Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 1123
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -2004,48 +2139,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/bin/
+-rwxr-xr-x root/root 67696 2016-04-26 12:33 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 67672 2016-04-26 12:33 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 67672 2016-04-26 12:33 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 67704 2016-04-26 12:33 ./usr/bin/md5fa
+-rwxr-xr-x root/root 67632 2016-04-26 12:33 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 528424 2016-04-26 12:33 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 67784 2016-04-26 12:33 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 12:33 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 12:33 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 12:33 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 12:33 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 12:33 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -2065,23 +2200,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: ppc64el
-Build-Space: 42548
-Build-Time: 200
+Build-Space: 42880
+Build-Time: 147
Distribution: sid
Host Architecture: ppc64el
-Install-Time: 11
-Job: samtools_1.3-1
+Install-Time: 12
+Job: samtools_1.3.1-1
Machine Architecture: ppc64el
Package: samtools
-Package-Time: 229
-Source-Version: 1.3-1
-Space: 42548
+Package-Time: 189
+Source-Version: 1.3.1-1
+Space: 42880
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1637
-Build needed 00:03:49, 42548k disc space
-Signature with key 'AE6C7FBC' requested:
- signfile /home/buildd/build/samtools_1.3-1_ppc64el.changes AE6C7FBC
+Finished at 20160426-1233
+Build needed 00:03:09, 42880k disc space
+Signature with key 'B2A6EE77' requested:
+ signfile /home/buildd/build/samtools_1.3.1-1_ppc64el.changes B2A6EE77
Successfully signed changes file
diff --git a/sh4.log b/sh4.log
index 5437aee..320201e 100644
--- a/sh4.log
+++ b/sh4.log
@@ -2,55 +2,37 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs95.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (sh4) 06 Feb 2016 18:40 ║
+║ samtools 1.3.1-1 (sh4) 26 Apr 2016 16:22 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: sh4
Build Architecture: sh4
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-I2xw7G/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-I2xw7G' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-sh4-sbuild-a534c10e-a8c3-42bd-a09b-84c305f65fb6' 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 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 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)
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [58.1 kB]
+Get:2 http://incoming.debian-ports.org/buildd unstable InRelease [43.3 kB]
+Get:3 ftp://ftp.debian.org/debian unstable InRelease [196 kB]
+Get:4 ftp://ftp.debian-ports.org/debian unstable InRelease [39.0 kB]
+Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [103 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unreleased InRelease [54.6 kB]
+Get:7 ftp://ftp.debian.org/debian unstable/main Sources.diff/Index [27.9 kB]
+Get:8 ftp://ftp.debian.org/debian unstable/main Sources [6767 kB]
+Get:9 http://incoming.debian-ports.org/buildd unstable/main sh4 Packages [96.0 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main sh4 Packages [13.9 MB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main all Packages [7170 kB]
+Fetched 28.5 MB in 55s (515 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -68,18 +50,16 @@ 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
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 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)
+Need to get 3771 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://incoming.debian.org/debian-buildd buildd-unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 1s (2822 kB/s)
Download complete and in download only mode
Check architectures
@@ -91,19 +71,19 @@ 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-0Pebpf/apt_archive/sbuild-build-depends-core-dummy.deb'.
-Unsupported ioctl: cmd=0x40049409
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-z7JnQP/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ Packages [525 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-z7JnQP/apt_archive/./Release.gpg: Signature by key E5261DE95945F5CD35A9B3572275F7C5A802BCC3 uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -118,16 +98,16 @@ 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 4 not upgraded.
+0 upgraded, 3 newly installed, 0 to remove and 45 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-0Pebpf/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [766 B]
+Get:1 file:/«BUILDDIR»/resolver-z7JnQP/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 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 (32.5 kB/s)
+Fetched 130 kB in 4s (31.7 kB/s)
Selecting previously unselected package libfakeroot:sh4.
-(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(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 ... 12907 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 ... 12959 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.
@@ -141,21 +121,21 @@ 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 (>= 1.3), 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
+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-o1J_GE/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-o1J_GE/apt_archive ./ Packages [741 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-o1J_GE/apt_archive/./Release.gpg: Signature by key E5261DE95945F5CD35A9B3572275F7C5A802BCC3 uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -167,67 +147,102 @@ 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 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file groff-base
+ intltool-debian libarchive-zip-perl libbsd0 libcurl3-gnutls
+ libfile-stripnondeterminism-perl libgnutls30 libgssapi-krb5-2 libhogweed4
+ libhts-dev libhts1 libidn11 libio-pty-perl libk5crypto3 libkeyutils1
+ libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool m4 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- gnu-standards autoconf-doc libtool wamerican | wordlist whois vacation
- dh-make groff ncurses-doc less www-browser libmail-box-perl
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make groff
+ gnutls-bin krb5-doc krb5-user ncurses-doc libtool-doc gfortran
+ | fortran95-compiler gcj-jdk less www-browser libmail-box-perl
Recommended packages:
+ ca-certificates krb5-locales libsasl2-modules libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
- 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
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file groff-base
+ intltool-debian libarchive-zip-perl libbsd0 libcurl3-gnutls
+ libfile-stripnondeterminism-perl libgnutls30 libgssapi-krb5-2 libhogweed4
+ libhts-dev libhts1 libidn11 libio-pty-perl libk5crypto3 libkeyutils1
+ libkrb5-3 libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool m4 man-db po-debconf
sbuild-build-depends-samtools-dummy tabix zlib1g-dev
-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]
+0 upgraded, 51 newly installed, 0 to remove and 45 not upgraded.
+Need to get 12.5 MB/12.5 MB of archives.
+After this operation, 38.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-o1J_GE/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 1:2.1-4.3 [178 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 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]
+Get:4 ftp://ftp.debian-ports.org/debian unstable/main sh4 libbsd0 sh4 0.8.3-1 [99.5 kB]
+Get:5 ftp://ftp.debian-ports.org/debian unstable/main sh4 bsdmainutils sh4 9.0.10 [186 kB]
+Get:6 ftp://ftp.debian-ports.org/debian unstable/main sh4 libpipeline1 sh4 1.4.1-2 [30.8 kB]
+Get:7 ftp://ftp.debian-ports.org/debian unstable/main sh4 man-db sh4 2.7.5-1 [1007 kB]
+Get:8 ftp://ftp.debian-ports.org/debian unstable/main sh4 autoconf-archive all 20150925-1 [688 kB]
+Get:9 ftp://ftp.debian-ports.org/debian unstable/main sh4 libssl1.0.2 sh4 1.0.2g-2 [1064 kB]
+Get:10 ftp://ftp.debian-ports.org/debian unstable/main sh4 libmagic1 sh4 1:5.25-2 [264 kB]
+Get:11 ftp://ftp.debian-ports.org/debian unstable/main sh4 file sh4 1:5.25-2 [61.5 kB]
+Get:12 ftp://ftp.debian-ports.org/debian unstable/main sh4 libnettle6 sh4 3.2-1 [217 kB]
+Get:13 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhogweed4 sh4 3.2-1 [133 kB]
+Get:14 ftp://ftp.debian-ports.org/debian unstable/main sh4 libidn11 sh4 1.32-3 [113 kB]
+Get:15 ftp://ftp.debian-ports.org/debian unstable/main sh4 libp11-kit0 sh4 0.23.2-3 [112 kB]
+Get:16 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtasn1-6 sh4 4.8-1 [52.2 kB]
+Get:17 ftp://ftp.debian-ports.org/debian unstable/main sh4 libgnutls30 sh4 3.4.11-3 [796 kB]
+Get:18 ftp://ftp.debian-ports.org/debian unstable/main sh4 libkeyutils1 sh4 1.5.9-8 [12.1 kB]
+Get:19 ftp://ftp.debian-ports.org/debian unstable/main sh4 libkrb5support0 sh4 1.13.2+dfsg-5 [59.8 kB]
+Get:20 ftp://ftp.debian-ports.org/debian unstable/main sh4 libk5crypto3 sh4 1.13.2+dfsg-5 [120 kB]
+Get:21 ftp://ftp.debian-ports.org/debian unstable/main sh4 libkrb5-3 sh4 1.13.2+dfsg-5 [318 kB]
+Get:22 ftp://ftp.debian-ports.org/debian unstable/main sh4 libgssapi-krb5-2 sh4 1.13.2+dfsg-5 [161 kB]
+Get:23 ftp://ftp.debian-ports.org/debian unstable/main sh4 libsasl2-modules-db sh4 2.1.26.dfsg1-15 [66.7 kB]
+Get:24 ftp://ftp.debian-ports.org/debian unstable/main sh4 libsasl2-2 sh4 2.1.26.dfsg1-15 [106 kB]
+Get:25 ftp://ftp.debian-ports.org/debian unstable/main sh4 libldap-2.4-2 sh4 2.4.42+dfsg-2+b2 [224 kB]
+Get:26 ftp://ftp.debian-ports.org/debian unstable/main sh4 libsigsegv2 sh4 2.10-5 [29.2 kB]
+Get:27 ftp://ftp.debian-ports.org/debian unstable/main sh4 m4 sh4 1.4.17-5 [250 kB]
+Get:28 ftp://ftp.debian-ports.org/debian unstable/main sh4 autoconf all 2.69-10 [338 kB]
+Get:29 ftp://ftp.debian-ports.org/debian unstable/main sh4 autotools-dev all 20150820.1 [71.7 kB]
+Get:30 ftp://ftp.debian-ports.org/debian unstable/main sh4 automake all 1:1.15-4 [735 kB]
+Get:31 ftp://ftp.debian-ports.org/debian unreleased/main sh4 autopoint all 0.19.7-2+sh4 [424 kB]
+Get:32 ftp://ftp.debian-ports.org/debian unstable/main sh4 intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:33 ftp://ftp.debian-ports.org/debian unstable/main sh4 po-debconf all 1.0.19 [249 kB]
+Get:34 ftp://ftp.debian-ports.org/debian unstable/main sh4 libarchive-zip-perl all 1.57-1 [95.1 kB]
+Get:35 ftp://ftp.debian-ports.org/debian unstable/main sh4 libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
+Get:36 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtimedate-perl all 2.3000-2 [42.2 kB]
+Get:37 ftp://ftp.debian-ports.org/debian unstable/main sh4 dh-strip-nondeterminism all 0.016-1 [6998 B]
+Get:38 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtool all 2.4.6-0.1 [200 kB]
+Get:39 ftp://ftp.debian-ports.org/debian unstable/main sh4 dh-autoreconf all 12 [15.8 kB]
+Get:40 ftp://ftp.debian-ports.org/debian unstable/main sh4 debhelper all 9.20160403 [800 kB]
+Get:41 ftp://ftp.debian-ports.org/debian unstable/main sh4 libnghttp2-14 sh4 1.9.2-1 [77.0 kB]
+Get:42 ftp://ftp.debian-ports.org/debian unstable/main sh4 librtmp1 sh4 2.4+20151223.gitfa8646d-1+b1 [64.3 kB]
+Get:43 ftp://ftp.debian-ports.org/debian unstable/main sh4 libssh2-1 sh4 1.5.0-2.1 [137 kB]
+Get:44 ftp://ftp.debian-ports.org/debian unstable/main sh4 libcurl3-gnutls sh4 7.47.0-1 [301 kB]
+Get:45 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts1 sh4 1.3.1-1 [278 kB]
+Get:46 ftp://ftp.debian-ports.org/debian unstable/main sh4 libhts-dev sh4 1.3.1-1 [316 kB]
+Get:47 ftp://ftp.debian-ports.org/debian unstable/main sh4 libio-pty-perl sh4 1:1.08-1.1 [34.6 kB]
+Get:48 ftp://ftp.debian-ports.org/debian unstable/main sh4 libtinfo-dev sh4 6.0+20160319-1 [72.9 kB]
+Get:49 ftp://ftp.debian-ports.org/debian unstable/main sh4 libncurses5-dev sh4 6.0+20160319-1 [165 kB]
+Get:50 ftp://ftp.debian-ports.org/debian unstable/main sh4 tabix sh4 1.3.1-1 [242 kB]
+Get:51 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 7656 kB in 56s (135 kB/s)
+Fetched 12.5 MB in 1min 40s (125 kB/s)
Selecting previously unselected package bash-completion.
-(Reading database ...
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 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) ...
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 13008 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.3-7_sh4.deb ...
Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:sh4.
+Preparing to unpack .../libbsd0_0.8.3-1_sh4.deb ...
+Unpacking libbsd0:sh4 (0.8.3-1) ...
Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6+b1_sh4.deb ...
-Unpacking bsdmainutils (9.0.6+b1) ...
+Preparing to unpack .../bsdmainutils_9.0.10_sh4.deb ...
+Unpacking bsdmainutils (9.0.10) ...
Selecting previously unselected package libpipeline1:sh4.
Preparing to unpack .../libpipeline1_1.4.1-2_sh4.deb ...
Unpacking libpipeline1:sh4 (1.4.1-2) ...
@@ -237,27 +252,75 @@ 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:sh4.
-Preparing to unpack .../libsigsegv2_2.10-4_sh4.deb ...
-Unpacking libsigsegv2:sh4 (2.10-4) ...
+Selecting previously unselected package libssl1.0.2:sh4.
+Preparing to unpack .../libssl1.0.2_1.0.2g-2_sh4.deb ...
+Unpacking libssl1.0.2:sh4 (1.0.2g-2) ...
Selecting previously unselected package libmagic1:sh4.
Preparing to unpack .../libmagic1_1%3a5.25-2_sh4.deb ...
Unpacking libmagic1:sh4 (1:5.25-2) ...
Selecting previously unselected package file.
Preparing to unpack .../file_1%3a5.25-2_sh4.deb ...
Unpacking file (1:5.25-2) ...
+Selecting previously unselected package libnettle6:sh4.
+Preparing to unpack .../libnettle6_3.2-1_sh4.deb ...
+Unpacking libnettle6:sh4 (3.2-1) ...
+Selecting previously unselected package libhogweed4:sh4.
+Preparing to unpack .../libhogweed4_3.2-1_sh4.deb ...
+Unpacking libhogweed4:sh4 (3.2-1) ...
+Selecting previously unselected package libidn11:sh4.
+Preparing to unpack .../libidn11_1.32-3_sh4.deb ...
+Unpacking libidn11:sh4 (1.32-3) ...
+Selecting previously unselected package libp11-kit0:sh4.
+Preparing to unpack .../libp11-kit0_0.23.2-3_sh4.deb ...
+Unpacking libp11-kit0:sh4 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:sh4.
+Preparing to unpack .../libtasn1-6_4.8-1_sh4.deb ...
+Unpacking libtasn1-6:sh4 (4.8-1) ...
+Selecting previously unselected package libgnutls30:sh4.
+Preparing to unpack .../libgnutls30_3.4.11-3_sh4.deb ...
+Unpacking libgnutls30:sh4 (3.4.11-3) ...
+Selecting previously unselected package libkeyutils1:sh4.
+Preparing to unpack .../libkeyutils1_1.5.9-8_sh4.deb ...
+Unpacking libkeyutils1:sh4 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:sh4.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_sh4.deb ...
+Unpacking libkrb5support0:sh4 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:sh4.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_sh4.deb ...
+Unpacking libk5crypto3:sh4 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:sh4.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_sh4.deb ...
+Unpacking libkrb5-3:sh4 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:sh4.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_sh4.deb ...
+Unpacking libgssapi-krb5-2:sh4 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:sh4.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_sh4.deb ...
+Unpacking libsasl2-modules-db:sh4 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:sh4.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_sh4.deb ...
+Unpacking libsasl2-2:sh4 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:sh4.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_sh4.deb ...
+Unpacking libldap-2.4-2:sh4 (2.4.42+dfsg-2+b2) ...
+Selecting previously unselected package libsigsegv2:sh4.
+Preparing to unpack .../libsigsegv2_2.10-5_sh4.deb ...
+Unpacking libsigsegv2:sh4 (2.10-5) ...
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) ...
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
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) ...
+Preparing to unpack .../automake_1%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2+sh4_all.deb ...
+Unpacking autopoint (0.19.7-2+sh4) ...
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) ...
@@ -265,78 +328,119 @@ 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) ...
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
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) ...
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
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) ...
+Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20160115_all.deb ...
-Unpacking debhelper (9.20160115) ...
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:sh4.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_sh4.deb ...
+Unpacking libnghttp2-14:sh4 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:sh4.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_sh4.deb ...
+Unpacking librtmp1:sh4 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:sh4.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_sh4.deb ...
+Unpacking libssh2-1:sh4 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:sh4.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_sh4.deb ...
+Unpacking libcurl3-gnutls:sh4 (7.47.0-1) ...
Selecting previously unselected package libhts1:sh4.
-Preparing to unpack .../archives/libhts1_1.3-1_sh4.deb ...
-Unpacking libhts1:sh4 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_sh4.deb ...
+Unpacking libhts1:sh4 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:sh4.
-Preparing to unpack .../libhts-dev_1.3-1_sh4.deb ...
-Unpacking libhts-dev:sh4 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_sh4.deb ...
+Unpacking libhts-dev:sh4 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:sh4.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_sh4.deb ...
-Unpacking libtinfo-dev:sh4 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_sh4.deb ...
+Unpacking libtinfo-dev:sh4 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_sh4.deb ...
+Unpacking libncurses5-dev:sh4 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_sh4.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../archives/tabix_1.3.1-1_sh4.deb ...
+Unpacking tabix (1.3.1-1) ...
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 (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-4) ...
+Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-7) ...
-Setting up bsdmainutils (9.0.6+b1) ...
+Setting up libbsd0:sh4 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
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 autoconf-archive (20150925-1) ...
-Setting up libsigsegv2:sh4 (2.10-4) ...
+Setting up libssl1.0.2:sh4 (1.0.2g-2) ...
Setting up libmagic1:sh4 (1:5.25-2) ...
Setting up file (1:5.25-2) ...
+Setting up libnettle6:sh4 (3.2-1) ...
+Setting up libhogweed4:sh4 (3.2-1) ...
+Setting up libidn11:sh4 (1.32-3) ...
+Setting up libp11-kit0:sh4 (0.23.2-3) ...
+Setting up libtasn1-6:sh4 (4.8-1) ...
+Setting up libgnutls30:sh4 (3.4.11-3) ...
+Setting up libkeyutils1:sh4 (1.5.9-8) ...
+Setting up libkrb5support0:sh4 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:sh4 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:sh4 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:sh4 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:sh4 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:sh4 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:sh4 (2.4.42+dfsg-2+b2) ...
+Setting up libsigsegv2:sh4 (2.10-5) ...
Setting up m4 (1.4.17-5) ...
-Setting up autoconf (2.69-9) ...
+Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
-Setting up automake (1:1.15-3) ...
+Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up autopoint (0.19.7-2+sh4) ...
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 libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
-Setting up libhts1:sh4 (1.3-1) ...
-Setting up libhts-dev:sh4 (1.3-1) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:sh4 (1.9.2-1) ...
+Setting up librtmp1:sh4 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:sh4 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:sh4 (7.47.0-1) ...
+Setting up libhts1:sh4 (1.3.1-1) ...
+Setting up libhts-dev:sh4 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:sh4 (6.0+20160319-1) ...
+Setting up libncurses5-dev:sh4 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
Setting up zlib1g-dev:sh4 (1:1.2.8.dfsg-2+b1) ...
-Setting up debhelper (9.20160115) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
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) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-4) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -344,8 +448,8 @@ 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_2.26-2 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 [...]
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-12 gcc-5_5.3.1-12 libc6-dev_2.22-4 libstdc++-5-dev_5.3.1-12 libstdc++6_5.3.1-12 linux-libc-dev_4.4.6-1
+Package versions: adduser_3.114 apt_1.2.8 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2+sh4 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_12.2 bzip2_1.0.6-8+b1 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-12 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debian-ports-archive-ke [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -356,12 +460,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -383,22 +487,22 @@ SCHROOT_CHROOT_NAME=sid-sh4-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-sh4-sbuild-496666af-b742-41be-9ef6-535f3ec4abe5
+SCHROOT_SESSION_ID=sid-sh4-sbuild-a534c10e-a8c3-42bd-a09b-84c305f65fb6
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c28
+XDG_SESSION_ID=c17
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture sh4
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -445,15 +549,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -465,6 +569,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -485,82 +591,82 @@ dh_auto_build -- \
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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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»'
@@ -661,7 +767,7 @@ Unsupported ioctl: cmd=0x40049409
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
+ (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
@@ -696,7 +802,7 @@ 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/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)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/wgsim 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
@@ -712,14 +818,14 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/samtools/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_sh4.deb'.
- dpkg-genchanges -B -mdebian/sh4 buildd <buildd-vs95 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3-1_sh4.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_sh4.deb'.
+ dpkg-genchanges -B -mdebian/sh4 buildd <buildd-vs95 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3.1-1_sh4.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160206-1858
+Build finished at 20160426-1639
Finished
────────
@@ -736,60 +842,52 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_sh4.changes:
-───────────────────────────
+samtools_1.3.1-1_sh4.changes:
+─────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: sh4
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
Maintainer: debian/sh4 buildd <buildd-vs95 at glaubitz.dialup.fu-berlin.de>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- b873560655af587fb26dee0d8f15f4aac3089819 253890 samtools_1.3-1_sh4.deb
+ d5559f6bcb41c9be24213d5e96b8c9e579c9630d 258736 samtools_1.3.1-1_sh4.deb
Checksums-Sha256:
- b6a69c6fca65a4914396e79bef4e07264b5577ebe6effa85bdbd08852085bcf3 253890 samtools_1.3-1_sh4.deb
+ 2697f5a3032a114bda098ccec11c4183ba610f399acb5f24c2157d81f692d5b0 258736 samtools_1.3.1-1_sh4.deb
Files:
- 8344f6c4519ad212d651a917ddd07105 253890 science optional samtools_1.3-1_sh4.deb
+ c53b5345a1296067f12a3a67465392aa 258736 science optional samtools_1.3.1-1_sh4.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_sh4.deb
-──────────────────────
+samtools_1.3.1-1_sh4.deb
+────────────────────────
new debian package, version 2.0.
- size 253890 bytes: control archive=1637 bytes.
- 805 bytes, 17 lines control
+ size 258736 bytes: control archive=1640 bytes.
+ 807 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: sh4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 604
- Depends: libc6 (>= 2.21), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 611
+ Depends: libc6 (>= 2.22), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -802,48 +900,48 @@ samtools_1.3-1_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 2016-02-06 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
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/bin/
+-rwxr-xr-x root/root 13652 2016-04-26 16:38 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 11:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 11:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 11:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 11:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9544 2016-04-26 16:38 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9544 2016-04-26 16:38 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9564 2016-04-26 16:38 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5432 2016-04-26 16:38 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 11:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 11:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 11:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 11:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 346520 2016-04-26 16:38 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 11:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 11:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 11:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 11:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17816 2016-04-26 16:38 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 11:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 11:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 11:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 13:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 13:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 14:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 13:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 13:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 13:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 16:38 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 16:38 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 16:38 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 16:38 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 16:38 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -863,23 +961,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: sh4
-Build-Space: 15376
-Build-Time: 765
+Build-Space: 15464
+Build-Time: 697
Distribution: sid
Host Architecture: sh4
-Install-Time: 211
-Job: samtools_1.3-1
+Install-Time: 217
+Job: samtools_1.3.1-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 1071
-Source-Version: 1.3-1
-Space: 15376
+Package-Time: 996
+Source-Version: 1.3.1-1
+Space: 15464
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160206-1858
-Build needed 00:17:51, 15376k disc space
+Finished at 20160426-1639
+Build needed 00:16:36, 15464k disc space
Signature with key '933A5126' requested:
- signfile /var/lib/buildd/build/samtools_1.3-1_sh4.changes 933A5126
+ signfile /var/lib/buildd/build/samtools_1.3.1-1_sh4.changes 933A5126
Successfully signed changes file
diff --git a/x32.log b/x32.log
index 86e19a1..61fca6a 100644
--- a/x32.log
+++ b/x32.log
@@ -2,49 +2,30 @@
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs76.physik.fu-berlin.de
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.3-1 (x32) 05 Feb 2016 17:45 ║
+║ samtools 1.3.1-1 (x32) 26 Apr 2016 23:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.3-1
-Source Version: 1.3-1
+Version: 1.3.1-1
+Source Version: 1.3.1-1
Distribution: sid
Machine Architecture: amd64
Host Architecture: x32
Build Architecture: x32
-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»'
+I: NOTICE: Log filtering will replace 'build/samtools-nLGq1P/samtools-1.3.1' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-nLGq1P' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-5e2c16d4-f6d8-47bb-b129-6ee0432c0d9a' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-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)
+Hit:1 http://ftp.debian.org/debian unstable InRelease
+Hit:2 http://incoming.debian-ports.org/buildd unstable InRelease
+Hit:3 http://ftp.debian-ports.org/debian unstable InRelease
+Hit:4 http://incoming.debian.org/debian-buildd buildd-unstable InRelease
+Hit:5 http://ftp.debian-ports.org/debian unreleased InRelease
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
@@ -62,18 +43,16 @@ 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
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 1s (2140 kB/s)
+Need to get 3771 kB of source archives.
+Get:1 http://ftp.debian.org/debian unstable/main samtools 1.3.1-1 (dsc) [2164 B]
+Get:2 http://ftp.debian.org/debian unstable/main samtools 1.3.1-1 (tar) [3757 kB]
+Get:3 http://ftp.debian.org/debian unstable/main samtools 1.3.1-1 (diff) [11.9 kB]
+Fetched 3771 kB in 0s (12.3 MB/s)
Download complete and in download only mode
Check architectures
@@ -85,18 +64,19 @@ 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-MmlFD4/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-hjDhfS/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Sources [208 B]
+Get:5 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ Packages [526 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-hjDhfS/apt_archive/./Release.gpg: Signature by key 74F48A4F3ED0864D7E205027E01082FBE9A662D5 uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -111,16 +91,13 @@ 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 11 not upgraded.
-Need to get 129 kB/130 kB of archives.
+0 upgraded, 3 newly installed, 0 to remove and 6 not upgraded.
+Need to get 0 B/130 kB of archives.
After this operation, 411 kB of additional disk space will be used.
-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]
+Get:1 file:/«BUILDDIR»/resolver-hjDhfS/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [762 B]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 129 kB in 1s (114 kB/s)
Selecting previously unselected package libfakeroot:x32.
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+(Reading database ...
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Preparing to unpack .../libfakeroot_1.20.2-1_x32.deb ...
Unpacking libfakeroot:x32 (1.20.2-1) ...
Selecting previously unselected package fakeroot.
@@ -129,26 +106,26 @@ 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
-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'.
+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-ewciQ6/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
-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]
+Get:1 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ InRelease
+Ign:1 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ InRelease
+Get:2 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Release [2119 B]
+Get:2 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Release [2119 B]
+Get:3 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Release.gpg [299 B]
+Get:3 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Release.gpg [299 B]
+Get:4 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Sources [484 B]
+Get:5 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ Packages [747 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+W: file:///«BUILDDIR»/resolver-ewciQ6/apt_archive/./Release.gpg: Signature by key 74F48A4F3ED0864D7E205027E01082FBE9A662D5 uses weak digest algorithm (SHA1)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -160,76 +137,298 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
- autoconf-archive bash-completion libhts-dev libhts1 libio-pty-perl
- libncurses5-dev libtinfo-dev tabix
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf tabix zlib1g-dev
Suggested packages:
- ncurses-doc
+ gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
+ gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
+ krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
+ www-browser libmail-box-perl
+Recommended packages:
+ curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
+ xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core
+ libmail-sendmail-perl
The following NEW packages will be installed:
- 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 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]
+ autoconf autoconf-archive automake autopoint autotools-dev bash-completion
+ bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
+ gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
+ libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
+ libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
+ libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
+ libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
+ libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
+ libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
+ libtimedate-perl libtinfo-dev libtool libunistring0 libxml2 m4 man-db
+ po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
+0 upgraded, 59 newly installed, 0 to remove and 6 not upgraded.
+Need to get 178 kB/25.9 MB of archives.
+After this operation, 87.2 MB of additional disk space will be used.
+Get:1 file:/«BUILDDIR»/resolver-ewciQ6/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [980 B]
+Get:2 http://ftp.debian-ports.org/debian unstable/main x32 bash-completion all 1:2.1-4.3 [178 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 1929 kB in 3s (594 kB/s)
+Fetched 178 kB in 1s (138 kB/s)
Selecting previously unselected package bash-completion.
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(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) ...
+(Reading database ...
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(Reading database ... 12336 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.3_all.deb ...
+Unpacking bash-completion (1:2.1-4.3) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-7_x32.deb ...
+Unpacking groff-base (1.22.3-7) ...
+Selecting previously unselected package libbsd0:x32.
+Preparing to unpack .../libbsd0_0.8.3-1_x32.deb ...
+Unpacking libbsd0:x32 (0.8.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.10_x32.deb ...
+Unpacking bsdmainutils (9.0.10) ...
+Selecting previously unselected package libpipeline1:x32.
+Preparing to unpack .../libpipeline1_1.4.1-2_x32.deb ...
+Unpacking libpipeline1:x32 (1.4.1-2) ...
+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 autoconf-archive.
Preparing to unpack .../autoconf-archive_20150925-1_all.deb ...
Unpacking autoconf-archive (20150925-1) ...
+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 libssl1.0.2:x32.
+Preparing to unpack .../libssl1.0.2_1.0.2f-2_x32.deb ...
+Unpacking libssl1.0.2:x32 (1.0.2f-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_0.19.7-2_x32.deb ...
+Unpacking gettext-base (0.19.7-2) ...
+Selecting previously unselected package libnettle6:x32.
+Preparing to unpack .../libnettle6_3.2-1_x32.deb ...
+Unpacking libnettle6:x32 (3.2-1) ...
+Selecting previously unselected package libhogweed4:x32.
+Preparing to unpack .../libhogweed4_3.2-1_x32.deb ...
+Unpacking libhogweed4:x32 (3.2-1) ...
+Selecting previously unselected package libidn11:x32.
+Preparing to unpack .../libidn11_1.32-3_x32.deb ...
+Unpacking libidn11:x32 (1.32-3) ...
+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 libp11-kit0:x32.
+Preparing to unpack .../libp11-kit0_0.23.2-3_x32.deb ...
+Unpacking libp11-kit0:x32 (0.23.2-3) ...
+Selecting previously unselected package libtasn1-6:x32.
+Preparing to unpack .../libtasn1-6_4.8-1_x32.deb ...
+Unpacking libtasn1-6:x32 (4.8-1) ...
+Selecting previously unselected package libgnutls30:x32.
+Preparing to unpack .../libgnutls30_3.4.11-4_x32.deb ...
+Unpacking libgnutls30:x32 (3.4.11-4) ...
+Selecting previously unselected package libkeyutils1:x32.
+Preparing to unpack .../libkeyutils1_1.5.9-8_x32.deb ...
+Unpacking libkeyutils1:x32 (1.5.9-8) ...
+Selecting previously unselected package libkrb5support0:x32.
+Preparing to unpack .../libkrb5support0_1.13.2+dfsg-5_x32.deb ...
+Unpacking libkrb5support0:x32 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libk5crypto3:x32.
+Preparing to unpack .../libk5crypto3_1.13.2+dfsg-5_x32.deb ...
+Unpacking libk5crypto3:x32 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libkrb5-3:x32.
+Preparing to unpack .../libkrb5-3_1.13.2+dfsg-5_x32.deb ...
+Unpacking libkrb5-3:x32 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libgssapi-krb5-2:x32.
+Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-5_x32.deb ...
+Unpacking libgssapi-krb5-2:x32 (1.13.2+dfsg-5) ...
+Selecting previously unselected package libsasl2-modules-db:x32.
+Preparing to unpack .../libsasl2-modules-db_2.1.26.dfsg1-15_x32.deb ...
+Unpacking libsasl2-modules-db:x32 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libsasl2-2:x32.
+Preparing to unpack .../libsasl2-2_2.1.26.dfsg1-15_x32.deb ...
+Unpacking libsasl2-2:x32 (2.1.26.dfsg1-15) ...
+Selecting previously unselected package libldap-2.4-2:x32.
+Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2+b2_x32.deb ...
+Unpacking libldap-2.4-2:x32 (2.4.42+dfsg-2+b2) ...
+Selecting previously unselected package libicu55:x32.
+Preparing to unpack .../libicu55_55.1-7_x32.deb ...
+Unpacking libicu55:x32 (55.1-7) ...
+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 libsigsegv2:x32.
+Preparing to unpack .../libsigsegv2_2.10-5_x32.deb ...
+Unpacking libsigsegv2:x32 (2.10-5) ...
+Selecting previously unselected package m4.
+Preparing to unpack .../archives/m4_1.4.17-5_x32.deb ...
+Unpacking m4 (1.4.17-5) ...
+Selecting previously unselected package autoconf.
+Preparing to unpack .../autoconf_2.69-10_all.deb ...
+Unpacking autoconf (2.69-10) ...
+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%3a1.15-4_all.deb ...
+Unpacking automake (1:1.15-4) ...
+Selecting previously unselected package autopoint.
+Preparing to unpack .../autopoint_0.19.7-2_all.deb ...
+Unpacking autopoint (0.19.7-2) ...
+Selecting previously unselected package libglib2.0-0:x32.
+Preparing to unpack .../libglib2.0-0_2.48.0-1_x32.deb ...
+Unpacking libglib2.0-0:x32 (2.48.0-1) ...
+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_0.19.7-2_x32.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_1.0.19_all.deb ...
+Unpacking po-debconf (1.0.19) ...
+Selecting previously unselected package libarchive-zip-perl.
+Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
+Unpacking libarchive-zip-perl (1.57-1) ...
+Selecting previously unselected package libfile-stripnondeterminism-perl.
+Preparing to unpack .../libfile-stripnondeterminism-perl_0.016-1_all.deb ...
+Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
+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_0.016-1_all.deb ...
+Unpacking dh-strip-nondeterminism (0.016-1) ...
+Selecting previously unselected package libtool.
+Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
+Unpacking libtool (2.4.6-0.1) ...
+Selecting previously unselected package dh-autoreconf.
+Preparing to unpack .../dh-autoreconf_12_all.deb ...
+Unpacking dh-autoreconf (12) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20160403_all.deb ...
+Unpacking debhelper (9.20160403) ...
+Selecting previously unselected package libnghttp2-14:x32.
+Preparing to unpack .../libnghttp2-14_1.9.2-1_x32.deb ...
+Unpacking libnghttp2-14:x32 (1.9.2-1) ...
+Selecting previously unselected package librtmp1:x32.
+Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_x32.deb ...
+Unpacking librtmp1:x32 (2.4+20151223.gitfa8646d-1+b1) ...
+Selecting previously unselected package libssh2-1:x32.
+Preparing to unpack .../libssh2-1_1.5.0-2.1_x32.deb ...
+Unpacking libssh2-1:x32 (1.5.0-2.1) ...
+Selecting previously unselected package libcurl3-gnutls:x32.
+Preparing to unpack .../libcurl3-gnutls_7.47.0-1_x32.deb ...
+Unpacking libcurl3-gnutls:x32 (7.47.0-1) ...
Selecting previously unselected package libhts1:x32.
-Preparing to unpack .../archives/libhts1_1.3-1_x32.deb ...
-Unpacking libhts1:x32 (1.3-1) ...
+Preparing to unpack .../libhts1_1.3.1-1_x32.deb ...
+Unpacking libhts1:x32 (1.3.1-1) ...
Selecting previously unselected package libhts-dev:x32.
-Preparing to unpack .../libhts-dev_1.3-1_x32.deb ...
-Unpacking libhts-dev:x32 (1.3-1) ...
+Preparing to unpack .../libhts-dev_1.3.1-1_x32.deb ...
+Unpacking libhts-dev:x32 (1.3.1-1) ...
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) ...
Selecting previously unselected package libtinfo-dev:x32.
-Preparing to unpack .../libtinfo-dev_6.0+20151024-2_x32.deb ...
-Unpacking libtinfo-dev:x32 (6.0+20151024-2) ...
+Preparing to unpack .../libtinfo-dev_6.0+20160319-1_x32.deb ...
+Unpacking libtinfo-dev:x32 (6.0+20160319-1) ...
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) ...
+Preparing to unpack .../libncurses5-dev_6.0+20160319-1_x32.deb ...
+Unpacking libncurses5-dev:x32 (6.0+20160319-1) ...
Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.3-1_x32.deb ...
-Unpacking tabix (1.3-1) ...
+Preparing to unpack .../archives/tabix_1.3.1-1_x32.deb ...
+Unpacking tabix (1.3.1-1) ...
+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) ...
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) ...
-Processing triggers for libc-bin (2.21-7) ...
-Setting up bash-completion (1:2.1-4.2) ...
+Processing triggers for libc-bin (2.22-7) ...
+Setting up bash-completion (1:2.1-4.3) ...
+Setting up groff-base (1.22.3-7) ...
+Setting up libbsd0:x32 (0.8.3-1) ...
+Setting up bsdmainutils (9.0.10) ...
+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 (1.4.1-2) ...
+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 libhts1:x32 (1.3-1) ...
-Setting up libhts-dev:x32 (1.3-1) ...
+Setting up libunistring0:x32 (0.9.3-5.2) ...
+Setting up libssl1.0.2:x32 (1.0.2f-2) ...
+Setting up libmagic1:x32 (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
+Setting up gettext-base (0.19.7-2) ...
+Setting up libnettle6:x32 (3.2-1) ...
+Setting up libhogweed4:x32 (3.2-1) ...
+Setting up libidn11:x32 (1.32-3) ...
+Setting up libffi6:x32 (3.2.1-4) ...
+Setting up libp11-kit0:x32 (0.23.2-3) ...
+Setting up libtasn1-6:x32 (4.8-1) ...
+Setting up libgnutls30:x32 (3.4.11-4) ...
+Setting up libkeyutils1:x32 (1.5.9-8) ...
+Setting up libkrb5support0:x32 (1.13.2+dfsg-5) ...
+Setting up libk5crypto3:x32 (1.13.2+dfsg-5) ...
+Setting up libkrb5-3:x32 (1.13.2+dfsg-5) ...
+Setting up libgssapi-krb5-2:x32 (1.13.2+dfsg-5) ...
+Setting up libsasl2-modules-db:x32 (2.1.26.dfsg1-15) ...
+Setting up libsasl2-2:x32 (2.1.26.dfsg1-15) ...
+Setting up libldap-2.4-2:x32 (2.4.42+dfsg-2+b2) ...
+Setting up libicu55:x32 (55.1-7) ...
+Setting up libxml2:x32 (2.9.3+dfsg1-1) ...
+Setting up libsigsegv2:x32 (2.10-5) ...
+Setting up m4 (1.4.17-5) ...
+Setting up autoconf (2.69-10) ...
+Setting up autotools-dev (20150820.1) ...
+Setting up automake (1:1.15-4) ...
+update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
+Setting up autopoint (0.19.7-2) ...
+Setting up libglib2.0-0:x32 (2.48.0-1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:x32 (0.6.11-1) ...
+Setting up gettext (0.19.7-2) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.19) ...
+Setting up libarchive-zip-perl (1.57-1) ...
+Setting up libfile-stripnondeterminism-perl (0.016-1) ...
+Setting up libtimedate-perl (2.3000-2) ...
+Setting up libtool (2.4.6-0.1) ...
+Setting up libnghttp2-14:x32 (1.9.2-1) ...
+Setting up librtmp1:x32 (2.4+20151223.gitfa8646d-1+b1) ...
+Setting up libssh2-1:x32 (1.5.0-2.1) ...
+Setting up libcurl3-gnutls:x32 (7.47.0-1) ...
+Setting up libhts1:x32 (1.3.1-1) ...
+Setting up libhts-dev:x32 (1.3.1-1) ...
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 (1.3-1) ...
+Setting up libtinfo-dev:x32 (6.0+20160319-1) ...
+Setting up libncurses5-dev:x32 (6.0+20160319-1) ...
+Setting up tabix (1.3.1-1) ...
+Setting up zlib1g-dev:x32 (1:1.2.8.dfsg-2+b2) ...
+Setting up dh-autoreconf (12) ...
+Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.21-7) ...
+Setting up dh-strip-nondeterminism (0.016-1) ...
+Processing triggers for libc-bin (2.22-7) ...
W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 4.1.0-0.bpo.2-amd64 amd64 (x86_64)
-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 [...]
+Kernel: Linux 4.3.0-0.bpo.1-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-15 gcc-5_5.3.1-15 libc6-dev_2.22-7 libstdc++-5-dev_5.3.1-15 libstdc++6_6.0.1-2 linux-libc-dev_4.5.1-1
+Package versions: adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6 base-passwd_3.5.39 bash_4.3-14+b1 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.28-1 build-essential_12.2 bzip2_1.0.6-8 coreutils_8.25-2 cpp_4:5.3.1-1 cpp-5_5.3.1-15 dash_0.5.8-2.2 debconf_1.5.59 debconf-i18n_1.5.59 debhelper_9.20160403 debian-archive-keyring_2014.3 debianutils_4.7 dh-autoreconf_1 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -240,12 +439,12 @@ 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: Signature made Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
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: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
+dpkg-source: info: extracting samtools in samtools-1.3.1
+dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
@@ -258,34 +457,31 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=nobench nocheck
+DEB_BUILD_OPTIONS=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-x32-sbuild
SCHROOT_CHROOT_NAME=sid-x32-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=122
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-x32-sbuild-1a279431-3f8a-4b28-b779-88532cfff01f
+SCHROOT_SESSION_ID=sid-x32-sbuild-5e2c16d4-f6d8-47bb-b129-6ee0432c0d9a
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
-XDG_SESSION_ID=c18679
+XDG_SESSION_ID=c7
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.3-1
+dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.3
+ dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture x32
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -293,7 +489,7 @@ dh clean --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
touch config.mk
dh_auto_clean --
- make -j1 distclean
+ 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
@@ -332,15 +528,15 @@ dh build-arch --parallel
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
+configure.ac:42: 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
+configure.ac:42: the top level
autoconf
-configure.ac:40: warning: AC_CONFIG_SUBDIRS: you should use literals
+configure.ac:42: 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
+configure.ac:42: 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
@@ -352,6 +548,8 @@ 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 special C compiler options needed for large files... no
+checking for _FILE_OFFSET_BITS value needed for large files... no
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
@@ -370,91 +568,1229 @@ 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 -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 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
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -I. -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 -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
+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 -j4 test VERBOSE=1 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/mcPUUSeLvn/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/mcPUUSeLvn/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/mcPUUSeLvn/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/mcPUUSeLvn/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/mcPUUSeLvn/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/mcPUUSeLvn/large_chrom.bam
+
+ ERR:
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/mcPUUSeLvn/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/mcPUUSeLvn/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/mcPUUSeLvn/mpileup.bam.list -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/mcPUUSeLvn/mpileup.cram.list -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/mcPUUSeLvn/mpileup.bam.list -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/mcPUUSeLvn/mpileup.cram.list -f /tmp/mcPUUSeLvn/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/mcPUUSeLvn/mpileup.cram.list -f /tmp/mcPUUSeLvn/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/mcPUUSeLvn/mpileup.cram.list -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mcPUUSeLvn/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/mcPUUSeLvn/mpileup.ref.fa.gz -r17:1050-1060 /tmp/mcPUUSeLvn/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ 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
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools addreplacerg
+.. ok
+
+test_usage_subcommand:
+ samtools collate
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools quickcheck
+.. ok
+
+test_usage_subcommand:
+ samtools fastq
+.. ok
+
+test_usage_subcommand:
+ samtools fasta
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+.. ok
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+.. ok
+
+test_usage_subcommand:
+ samtools depad
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 2: SAM -> uncompressed BAM .. ok
+
+ 3: uncompressed BAM -> SAM and compare .. ok
+
+ 4: SAM -> fast compressed BAM .. ok
+
+ 5: fast compressed BAM -> SAM and compare .. ok
+
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
+
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 8: BAM -> CRAM with UR -> SAM .. ok
+
+ 9: SAM -> BAM (M5 header tags) .. ok
+
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
+
+ 11: CRAM -> BAM with UR .. ok
+
+ 12: CRAM -> BAM with M5 .. ok
+
+ 13: SAM -> SAM via stdout .. ok
+
+ 14: SAM -> BAM via stdout .. ok
+
+ 15: SAM -> CRAM via stdout .. ok
+
+ 16: SAM from stdin -> SAM .. ok
+
+ 17: BAM from stdin -> SAM .. ok
+
+ 18: CRAM from stdin -> SAM .. ok
+
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
+
+ 21: samtools view -H (CRAM input) .. ok
+
+ 22: No headers (SAM input) .. ok
+
+ 23: No headers (BAM input) .. ok
+
+ 24: No headers (CRAM input) .. ok
+
+ 25: Filter -f 128 (SAM input) .. ok
+
+ 26: Count -f 128 (SAM input) .. ok
+
+ 27: Filter -f 128 (BAM input) .. ok
+
+ 28: Count -f 128 (BAM input) .. ok
+
+ 29: Filter -f 128 (CRAM input) .. ok
+
+ 30: Count -f 128 (CRAM input) .. ok
+
+ 31: Filter -F 128 (SAM input) .. ok
+
+ 32: Count -F 128 (SAM input) .. ok
+
+ 33: Filter -F 128 (BAM input) .. ok
+
+ 34: Count -F 128 (BAM input) .. ok
+
+ 35: Filter -F 128 (CRAM input) .. ok
+
+ 36: Count -F 128 (CRAM input) .. ok
+
+ 37: Filter -F 128 -f 2 (SAM input) .. ok
+
+ 38: Count -F 128 -f 2 (SAM input) .. ok
+
+ 39: Filter -F 128 -f 2 (BAM input) .. ok
+
+ 40: Count -F 128 -f 2 (BAM input) .. ok
+
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
+
+ 42: Count -F 128 -f 2 (CRAM input) .. ok
+
+ 43: Filter -r grp2 (SAM input) .. ok
+
+ 44: Count -r grp2 (SAM input) .. ok
+
+ 45: Filter -r grp2 (BAM input) .. ok
+
+ 46: Count -r grp2 (BAM input) .. ok
+
+ 47: Filter -r grp2 (CRAM input) .. ok
+
+ 48: Count -r grp2 (CRAM input) .. ok
+
+ 49: Filter -R /tmp/mcPUUSeLvn/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/mcPUUSeLvn/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/mcPUUSeLvn/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/mcPUUSeLvn/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/mcPUUSeLvn/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/mcPUUSeLvn/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/mcPUUSeLvn/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/mcPUUSeLvn/view.001.fogn (CRAM input).. ok
+
+ 67: Filter -l Library 2 (SAM input) .. ok
+
+ 68: Count -l Library 2 (SAM input) .. ok
+
+ 69: Filter -l Library 2 (BAM input) .. ok
+
+ 70: Count -l Library 2 (BAM input) .. ok
+
+ 71: Filter -l Library 2 (CRAM input) .. ok
+
+ 72: Count -l Library 2 (CRAM input) .. ok
+
+ 73: Filter -l Library 3 (SAM input) .. ok
+
+ 74: Count -l Library 3 (SAM input) .. ok
+
+ 75: Filter -l Library 3 (BAM input) .. ok
+
+ 76: Count -l Library 3 (BAM input) .. ok
+
+ 77: Filter -l Library 3 (CRAM input) .. ok
+
+ 78: Count -l Library 3 (CRAM input) .. ok
+
+ 79: Filter -q 50 (SAM input) .. ok
+
+ 80: Count -q 50 (SAM input) .. ok
+
+ 81: Filter -q 50 (BAM input) .. ok
+
+ 82: Count -q 50 (BAM input) .. ok
+
+ 83: Filter -q 50 (CRAM input) .. ok
+
+ 84: Count -q 50 (CRAM input) .. ok
+
+ 85: Filter -q 99 (SAM input) .. ok
+
+ 86: Count -q 99 (SAM input) .. ok
+
+ 87: Filter -q 99 (BAM input) .. ok
+
+ 88: Count -q 99 (BAM input) .. ok
+
+ 89: Filter -q 99 (CRAM input) .. ok
+
+ 90: Count -q 99 (CRAM input) .. ok
+
+ 91: Filter -q 100 (SAM input) .. ok
+
+ 92: Count -q 100 (SAM input) .. ok
+
+ 93: Filter -q 100 (BAM input) .. ok
+
+ 94: Count -q 100 (BAM input) .. ok
+
+ 95: Filter -q 100 (CRAM input) .. ok
+
+ 96: Count -q 100 (CRAM input) .. ok
+
+ 97: Filter -x fa (SAM input) .. ok
+
+ 98: Count -x fa (SAM input) .. ok
+
+ 99: Filter -x fa (BAM input) .. ok
+
+ 100: Count -x fa (BAM input) .. ok
+
+ 101: Filter -x fa (CRAM input) .. ok
+
+ 102: Count -x fa (CRAM input) .. ok
+
+ 103: Filter -x fa -x ha (SAM input) .. ok
+
+ 104: Count -x fa -x ha (SAM input) .. ok
+
+ 105: Filter -x fa -x ha (BAM input) .. ok
+
+ 106: Count -x fa -x ha (BAM input) .. ok
+
+ 107: Filter -x fa -x ha (CRAM input) .. ok
+
+ 108: Count -x fa -x ha (CRAM input) .. ok
+
+ 109: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 110: Count -x fa -r grp2 (SAM input) .. ok
+
+ 111: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 112: Count -x fa -r grp2 (BAM input) .. ok
+
+ 113: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 114: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 115: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 116: Count -x RG -r grp2 (SAM input) .. ok
+
+ 117: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 118: Count -x RG -r grp2 (BAM input) .. ok
+
+ 119: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 120: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 121: Filter -m 10 (SAM input) .. ok
+
+ 122: Count -m 10 (SAM input) .. ok
+
+ 123: Filter -m 10 (BAM input) .. ok
+
+ 124: Count -m 10 (BAM input) .. ok
+
+ 125: Filter -m 10 (CRAM input) .. ok
+
+ 126: Count -m 10 (CRAM input) .. ok
+
+ 127: Filter -m 11 (SAM input) .. ok
+
+ 128: Count -m 11 (SAM input) .. ok
+
+ 129: Filter -m 11 (BAM input) .. ok
+
+ 130: Count -m 11 (BAM input) .. ok
+
+ 131: Filter -m 11 (CRAM input) .. ok
+
+ 132: Count -m 11 (CRAM input) .. ok
+
+ 133: Filter -m 15 (SAM input) .. ok
+
+ 134: Count -m 15 (SAM input) .. ok
+
+ 135: Filter -m 15 (BAM input) .. ok
+
+ 136: Count -m 15 (BAM input) .. ok
+
+ 137: Filter -m 15 (CRAM input) .. ok
+
+ 138: Count -m 15 (CRAM input) .. ok
+
+ 139: Filter -m 16 (SAM input) .. ok
+
+ 140: Count -m 16 (SAM input) .. ok
+
+ 141: Filter -m 16 (BAM input) .. ok
+
+ 142: Count -m 16 (BAM input) .. ok
+
+ 143: Filter -m 16 (CRAM input) .. ok
+
+ 144: Count -m 16 (CRAM input) .. ok
+
+ 145: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 146: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 146: Region Z (BAM input) .. ok
+
+ 147: Count Z (BAM input) .. ok
+
+ 148: Region Z (CRAM input) .. ok
+
+ 149: Count Z (CRAM input) .. ok
+
+ 150: Region Z:30 (BAM input) .. ok
+
+ 151: Count Z:30 (BAM input) .. ok
+
+ 152: Region Z:30 (CRAM input) .. ok
+
+ 153: Count Z:30 (CRAM input) .. ok
+
+ 154: Region Z:20-40 (BAM input) .. ok
+
+ 155: Count Z:20-40 (BAM input) .. ok
+
+ 156: Region Z:20-40 (CRAM input) .. ok
+
+ 157: Count Z:20-40 (CRAM input) .. ok
+
+ 158: Region ref1 (BAM input) .. ok
+
+ 159: Count ref1 (BAM input) .. ok
+
+ 160: Region ref1 (CRAM input) .. ok
+
+ 161: Count ref1 (CRAM input) .. ok
+
+ 162: Region ref1:15 (BAM input) .. ok
+
+ 163: Count ref1:15 (BAM input) .. ok
+
+ 164: Region ref1:15 (CRAM input) .. ok
+
+ 165: Count ref1:15 (CRAM input) .. ok
+
+ 166: Region ref1:15-45 (BAM input) .. ok
+
+ 167: Count ref1:15-45 (BAM input) .. ok
+
+ 168: Region ref1:15-45 (CRAM input) .. ok
+
+ 169: Count ref1:15-45 (CRAM input) .. ok
+
+ 170: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 171: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 172: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 173: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 186: Region -f 128 ref1 (BAM input) .. ok
+
+ 187: Count -f 128 ref1 (BAM input) .. ok
+
+ 188: Region -f 128 ref1 (CRAM input) .. ok
+
+ 189: Count -f 128 ref1 (CRAM input) .. ok
+
+ 190: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 191: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 192: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 193: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 194: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 195: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 198: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 199: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (BAM input).. ok
+
+ 200: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 201: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed (CRAM input).. ok
+
+ 202: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 203: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (BAM input).. ok
+
+ 204: Region -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 205: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
+
+ 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 207: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input).. ok
+
+ 208: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 209: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input).. ok
+
+ 210: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 211: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input).. ok
+
+ 212: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 213: Count -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input).. ok
+
+ 214: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 215: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (BAM input).. ok
+
+ 216: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 217: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z (CRAM input).. ok
+
+ 218: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 219: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (BAM input).. ok
+
+ 220: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 221: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
+
+ 222: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 223: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
+
+ 224: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 225: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
+
+ 226: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 227: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
+
+ 228: Region -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 229: Count -L /«PKGBUILDDIR»/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
+
+ 230: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 231: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
+
+ 232: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 233: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
+
+ 234: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 235: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (BAM input).. ok
+
+ 236: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 237: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref2 (CRAM input).. ok
+
+ 238: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 239: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
+
+ 240: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 241: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
+
+ 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 243: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (BAM input).. ok
+
+ 244: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 245: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
+
+ 246: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 247: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (BAM input).. ok
+
+ 248: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 249: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
+
+ 250: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 251: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
+
+ 252: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 253: Count -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 254: Make BAM with no M5/UR tags .. ok
+
+ 255: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 256: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 257: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 258: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 259: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 260: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 261: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 262: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 263: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 264: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 265: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 266: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 267: Make CRAM with no UR field .. ok
+
+ 268: Decoding CRAM with no UR field via -T .. ok
+
+ 269: CIGAR B-operator removal .. ok
+
+ 270: Big SAM -> BAM .. ok
+
+ 271: Big SAM -> BAM (2 threads) .. ok
+
+ 272: Big SAM -> BAM (4 threads) .. ok
+
+ 273: Big SAM -> CRAM .. ok
+
+ 274: Big SAM -> CRAM (2 threads) .. ok
+
+ 275: Big SAM -> CRAM (4 threads) .. ok
+
+ 276: Subsample 0.2 (SAM input) ............ ok
+
+ 277: Subsample 0.5 (SAM input) ............ ok
+
+ 278: Subsample 0.8 (SAM input) ............ ok
+
+ 279: Subsample 0.2 (BAM input) ............ ok
+
+ 280: Subsample 0.5 (BAM input) ............ ok
+
+ 281: Subsample 0.8 (BAM input) ............ ok
+
+ 282: Subsample 0.2 (CRAM input) ............ ok
+
+ 283: Subsample 0.5 (CRAM input) ............ ok
+
+ 284: Subsample 0.8 (CRAM input) ............ ok
+
+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 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
+
+ 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 .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 1: fastq (SAM input) .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 2: fastq -n (SAM input) .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 3: fastq (BAM input) .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 4: fastq -n (BAM input) .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 5: fastq (CRAM input) .. ok
+
+[M::bam2fq_mainloop] processed 36 reads
+ 6: fastq -n (CRAM input) .. ok
+
+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
+
+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
+
+test_depad:
+ Generate BAM file .. ok
+
+ depad (SAM input) .. ok
+
+ depad -s (SAM input) .. ok
+
+ depad -u (SAM input) .. ok
+
+ depad -1 (SAM input) .. ok
+
+ depad (BAM input) .. ok
+
+ depad -s (BAM input) .. ok
+
+ depad -u (BAM input) .. ok
+
+ 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
+
+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
+
+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/5_insert_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+4
+.. ok
+
+test_stats:
+ /«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/8_secondary.sam | tail -n+4
+.. ok
+
+test_stats:
+ /«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 -S RG -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/10_map_cigar.sam | tail -n+4
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
+.. ok
+
+test_merge:
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/jtD5vY4nb2 - /«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/mcPUUSeLvn/sortout
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -f /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/mcPUUSeLvn/sortout.bam
+.. ok
+
+test_sort:
+ /«PKGBUILDDIR»/samtools sort -o /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /tmp/mcPUUSeLvn/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:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/2_isize_overflow.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/3_reverse_read_pp_lt.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/4_reverse_read_pp_equal.sam -
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -cO sam /«PKGBUILDDIR»/test/fixmate/5_ct.sam -
+.. ok
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram
+
+ ERR:
+.. expected failure
+
+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 /«PKGBUILDDIR»/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
+
+ The outputs stdout differ:
+ /«PKGBUILDDIR»/test/quickcheck/all.expected
+ /«PKGBUILDDIR»/test/quickcheck/all.expected.new
+.. expected failure
+
+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 .. 423
+ passed .. 403
+ failed .. 0
+ expected failure .. 20
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh mpileup.reg
+
+=== Testing mpileup.reg regressions ===
+
+Expected passes: 124
+Unexpected passes: 0
+Expected failures: 0
+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
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
@@ -468,7 +1804,7 @@ 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 -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
@@ -504,15 +1840,15 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 ./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
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
@@ -520,7 +1856,7 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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
+ (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
@@ -543,55 +1879,54 @@ 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/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/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
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/50
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/50/06117ccbf3c116cc74e334401e9ad0e8cdb3a9.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/50/06117ccbf3c116cc74e334401e9ad0e8cdb3a9.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/50/06117ccbf3c116cc74e334401e9ad0e8cdb3a9.debug debian/samtools/usr/bin/wgsim
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/8a289a31ffd2a3d860b9dcf358ac029e95b8bc.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/8a289a31ffd2a3d860b9dcf358ac029e95b8bc.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/94/8a289a31ffd2a3d860b9dcf358ac029e95b8bc.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/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/29acdc3f9e2accab4272fa8143a2c436e61bf1.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/29acdc3f9e2accab4272fa8143a2c436e61bf1.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/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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/d1/29acdc3f9e2accab4272fa8143a2c436e61bf1.debug debian/samtools/usr/bin/ace2sam
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/543013a802c3f1b390b1d6992674d1aee6ef43.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/543013a802c3f1b390b1d6992674d1aee6ef43.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/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/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
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/543013a802c3f1b390b1d6992674d1aee6ef43.debug debian/samtools/usr/bin/maq2sam-short
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/d103442c4ad3703857562816c54e1ac0f28fc1.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/b9/d103442c4ad3703857562816c54e1ac0f28fc1.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/b9/d103442c4ad3703857562816c54e1ac0f28fc1.debug debian/samtools/usr/bin/samtools
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34/1e03cdac51b3cb092c02e225479965d6c70504.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34/1e03cdac51b3cb092c02e225479965d6c70504.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/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/dbgsym-root/usr/lib/debug/.build-id/91/d0f84f7603c0c4bb671d27fe95054c3a4119c3.debug debian/samtools/usr/bin/wgsim
+ objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/34/1e03cdac51b3cb092c02e225479965d6c70504.debug debian/samtools/usr/bin/md5sum-lite
+ install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ea
+ objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ea/60e396f3f8c78dbda6ffad514b74c10b4c4e72.debug
+ chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ea/60e396f3f8c78dbda6ffad514b74c10b4c4e72.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/ea/60e396f3f8c78dbda6ffad514b74c10b4c4e72.debug debian/samtools/usr/bin/maq2sam-long
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/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)
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/samtools debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam 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=0fa3dd0169f7ec30056c5c36d91e9b0233134794 142f52985ac22ad66759f0f83fec4416994b0cd0 5bc57d99e645c78814880119e811684b [...]
+ 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=341e03cdac51b3cb092c02e225479965d6c70504 5006117ccbf3c116cc74e334401e9ad0e8cdb3a9 948a289a31ffd2a3d860b9dcf358ac02 [...]
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
@@ -610,17 +1945,17 @@ dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
-dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3-1_x32.deb'.
+dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_x32.deb'.
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.3-1_x32.deb'.
- dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.3-1_x32.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_x32.deb'.
+ dpkg-genchanges -B -mDebian/x32 buildd <buildd-x32_vs76 at glaubitz.dialup.fu-berlin.de> >../samtools_1.3.1-1_x32.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.3
-dpkg-source: info: using options from samtools-1.3/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
+ dpkg-source --after-build samtools-1.3.1
+dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20160205-1746
+Build finished at 20160426-2309
Finished
────────
@@ -637,108 +1972,99 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.3-1_x32.changes:
-───────────────────────────
+samtools_1.3.1-1_x32.changes:
+─────────────────────────────
Format: 1.8
-Date: Fri, 05 Feb 2016 08:32:40 +0000
+Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: x32
-Version: 1.3-1
+Version: 1.3.1-1
Distribution: sid
Urgency: medium
-Maintainer: Debian/x32 buildd <buildd at vs76.physik.fu-berlin.de>
-Changed-By: Sascha Steinbiss <sascha at steinbiss.name>
+Maintainer: Debian/x32 buildd <buildd-x32_vs76 at glaubitz.dialup.fu-berlin.de>
+Changed-By: Charles Plessy <plessy at debian.org>
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
+ samtools (1.3.1-1) unstable; urgency=medium
.
- [ 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
+ 0c961b2 Merge tag '1.3.1' into debian/unstable
+ 3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
- 155fd711ba7c3310bc52dde7aabcb5796a545707 445664 samtools-dbgsym_1.3-1_x32.deb
- a8a6f4efae51c45b0c68d5a882ffc1f30c8de551 247346 samtools_1.3-1_x32.deb
+ 583433ed077f3dca892bf1ed06381c1bd8776d35 453948 samtools-dbgsym_1.3.1-1_x32.deb
+ 00cfb2af7c7bb39fa04bd8309e11eb8b357d7b6b 253034 samtools_1.3.1-1_x32.deb
Checksums-Sha256:
- 4a6c4e83618d4f1c22319d98e54223ef92039a0706b93a9d2a5b852f70836f99 445664 samtools-dbgsym_1.3-1_x32.deb
- 4611b15f5647ff1519c8b5b2cb91b64361d2a6351e622bbdd9ec0baeacec472d 247346 samtools_1.3-1_x32.deb
+ 8d173ee228f738a58c8bc27f84cb3e713187eaf5fc25ce8e310670ae0d8a6409 453948 samtools-dbgsym_1.3.1-1_x32.deb
+ 412dec5c3435cd55649a43b5f10dca4ec3eb88c9da3db59da474cae910103de2 253034 samtools_1.3.1-1_x32.deb
Files:
- bd478b2aa7b7c973f60b990d5ee9cedc 445664 debug extra samtools-dbgsym_1.3-1_x32.deb
- dbd556e7f7a5f5d000d8a2c47801dc05 247346 science optional samtools_1.3-1_x32.deb
+ 413d66b6d7ee40e20e4240ed800170ea 453948 debug extra samtools-dbgsym_1.3.1-1_x32.deb
+ 849d98c5ae5efb1b38b0b6d391723a6d 253034 science optional samtools_1.3.1-1_x32.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools-dbgsym_1.3-1_x32.deb
-─────────────────────────────
+samtools-dbgsym_1.3.1-1_x32.deb
+───────────────────────────────
new debian package, version 2.0.
- size 445664 bytes: control archive=816 bytes.
- 644 bytes, 13 lines control
+ size 453948 bytes: control archive=816 bytes.
+ 648 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: x32
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 499
- Depends: samtools (= 1.3-1)
+ Installed-Size: 507
+ Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
- Build-Ids: 0fa3dd0169f7ec30056c5c36d91e9b0233134794 142f52985ac22ad66759f0f83fec4416994b0cd0 5bc57d99e645c78814880119e811684bdfc7b71f 6a461ddf3a5d93f136464ae7f29a25ec75cb408a 8d624e41bd12e84898c21279727cbc725dd105a0 91d0f84f7603c0c4bb671d27fe95054c3a4119c3 9288e583a1aace174427b1eeeaa13837d8363461
-
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--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
-──────────────────────
+ Build-Ids: 341e03cdac51b3cb092c02e225479965d6c70504 5006117ccbf3c116cc74e334401e9ad0e8cdb3a9 948a289a31ffd2a3d860b9dcf358ac029e95b8bc b9543013a802c3f1b390b1d6992674d1aee6ef43 b9d103442c4ad3703857562816c54e1ac0f28fc1 d129acdc3f9e2accab4272fa8143a2c436e61bf1 ea60e396f3f8c78dbda6ffad514b74c10b4c4e72
+
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+-rw-r--r-- root/root 9756 2016-04-26 23:09 ./usr/lib/debug/.build-id/94/8a289a31ffd2a3d860b9dcf358ac029e95b8bc.debug
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+-rw-r--r-- root/root 428296 2016-04-26 23:09 ./usr/lib/debug/.build-id/b9/d103442c4ad3703857562816c54e1ac0f28fc1.debug
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+-rw-r--r-- root/root 9724 2016-04-26 23:09 ./usr/lib/debug/.build-id/ea/60e396f3f8c78dbda6ffad514b74c10b4c4e72.debug
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/doc/
+lrwxrwxrwx root/root 0 2016-04-26 23:09 ./usr/share/doc/samtools-dbgsym -> samtools
+
+
+samtools_1.3.1-1_x32.deb
+────────────────────────
new debian package, version 2.0.
- size 247346 bytes: control archive=1633 bytes.
+ size 253034 bytes: control archive=1634 bytes.
805 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
- Version: 1.3-1
+ Version: 1.3.1-1
Architecture: x32
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 681
- Depends: libc6 (>= 2.16), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 688
+ Depends: libc6 (>= 2.16), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.1.4)
Recommends: python
Section: science
Priority: optional
@@ -751,48 +2077,48 @@ samtools_1.3-1_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 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
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/bin/
+-rwxr-xr-x root/root 18056 2016-04-26 23:09 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2016-04-22 11:22 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2016-04-22 11:22 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2016-04-22 11:22 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2016-04-22 11:22 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9832 2016-04-26 23:09 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9832 2016-04-26 23:09 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 9872 2016-04-26 23:09 ./usr/bin/md5fa
+-rwxr-xr-x root/root 5704 2016-04-26 23:09 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2016-04-22 11:22 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48367 2016-04-22 11:22 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2016-04-22 11:22 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2016-04-22 11:22 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 421480 2016-04-26 23:09 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2016-04-22 11:22 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2016-04-22 11:22 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2016-04-22 11:22 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2016-04-22 11:22 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 18144 2016-04-26 23:09 ./usr/bin/wgsim
+-rwxr-xr-x root/root 12540 2016-04-22 11:22 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2016-04-22 11:22 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/doc/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2016-04-22 11:22 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 295 2016-04-26 13:47 ./usr/share/doc/samtools/NEWS.Debian.gz
+-rw-r--r-- root/root 721 2016-04-26 13:58 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3959 2016-04-26 14:12 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 2713 2016-04-26 13:47 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2016-04-26 13:47 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/lintian/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/lintian/overrides/
+-rw-r--r-- root/root 219 2016-04-26 13:47 ./usr/share/lintian/overrides/samtools
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/man/
+drwxr-xr-x root/root 0 2016-04-26 23:09 ./usr/share/man/man1/
+-rw-r--r-- root/root 462 2016-04-26 23:09 ./usr/share/man/man1/ace2sam.1.gz
+-rw-r--r-- root/root 19456 2016-04-26 23:09 ./usr/share/man/man1/samtools.1.gz
+-rw-r--r-- root/root 410 2016-04-26 23:09 ./usr/share/man/man1/samtools.pl.1.gz
+-rw-r--r-- root/root 518 2016-04-26 23:09 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -805,30 +2131,134 @@ drwxr-xr-x root/root 0 2016-02-05 17:46 ./usr/share/man/man1/
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
-Not cleaning session: cloned chroot in use
+Reading package lists...
+Building dependency tree...
+Reading state information...
+0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following packages will be REMOVED:
+ autoconf* autoconf-archive* automake* autopoint* autotools-dev*
+ bash-completion* bsdmainutils* debhelper* dh-autoreconf*
+ dh-strip-nondeterminism* fakeroot* file* gettext* gettext-base* groff-base*
+ intltool-debian* libarchive-zip-perl* libbsd0* libcroco3* libcurl3-gnutls*
+ libfakeroot* libffi6* libfile-stripnondeterminism-perl* libglib2.0-0*
+ libgnutls30* libgssapi-krb5-2* libhogweed4* libhts-dev* libhts1* libicu55*
+ libidn11* libio-pty-perl* libk5crypto3* libkeyutils1* libkrb5-3*
+ libkrb5support0* libldap-2.4-2* libmagic1* libncurses5-dev* libnettle6*
+ libnghttp2-14* libp11-kit0* libpipeline1* librtmp1* libsasl2-2*
+ libsasl2-modules-db* libsigsegv2* libssh2-1* libssl1.0.2* libtasn1-6*
+ libtimedate-perl* libtinfo-dev* libtool* libunistring0* libxml2* m4* man-db*
+ po-debconf* sbuild-build-depends-core-dummy*
+ sbuild-build-depends-samtools-dummy* tabix* zlib1g-dev*
+0 upgraded, 0 newly installed, 62 to remove and 6 not upgraded.
+After this operation, 87.6 MB disk space will be freed.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 16251 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 (1:2.1-4.3) ...
+Purging configuration files for bash-completion (1:2.1-4.3) ...
+Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
+Removing fakeroot (1.20.2-1) ...
+update-alternatives: using /usr/bin/fakeroot-tcp to provide /usr/bin/fakeroot (fakeroot) in auto mode
+Purging configuration files for fakeroot (1.20.2-1) ...
+Removing tabix (1.3.1-1) ...
+Removing libhts-dev:x32 (1.3.1-1) ...
+Removing libhts1:x32 (1.3.1-1) ...
+Removing libcurl3-gnutls:x32 (7.47.0-1) ...
+Removing libfakeroot:x32 (1.20.2-1) ...
+Purging configuration files for libfakeroot:x32 (1.20.2-1) ...
+dpkg: warning: while removing libfakeroot:x32, directory '/usr/lib/x86_64-linux-gnux32/libfakeroot' not empty so not removed
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+Purging configuration files for libldap-2.4-2:x32 (2.4.42+dfsg-2+b2) ...
+Removing libgnutls30:x32 (3.4.11-4) ...
+Removing libp11-kit0:x32 (0.23.2-3) ...
+Removing libgssapi-krb5-2:x32 (1.13.2+dfsg-5) ...
+Purging configuration files for libgssapi-krb5-2:x32 (1.13.2+dfsg-5) ...
+Removing libhogweed4:x32 (3.2-1) ...
+Removing libidn11:x32 (1.32-3) ...
+Purging configuration files for libidn11:x32 (1.32-3) ...
+Removing libio-pty-perl (1:1.08-1.1+b1) ...
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+Removing libk5crypto3:x32 (1.13.2+dfsg-5) ...
+Removing libkrb5support0:x32 (1.13.2+dfsg-5) ...
+Removing libkeyutils1:x32 (1.5.9-8) ...
+Removing libncurses5-dev:x32 (6.0+20160319-1) ...
+Removing libnettle6:x32 (3.2-1) ...
+Removing libnghttp2-14:x32 (1.9.2-1) ...
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+Removing libsasl2-modules-db:x32 (2.1.26.dfsg1-15) ...
+Removing libssh2-1:x32 (1.5.0-2.1) ...
+Removing libssl1.0.2:x32 (1.0.2f-2) ...
+Purging configuration files for libssl1.0.2:x32 (1.0.2f-2) ...
+Removing libtasn1-6:x32 (4.8-1) ...
+Removing libtinfo-dev:x32 (6.0+20160319-1) ...
+Removing zlib1g-dev:x32 (1:1.2.8.dfsg-2+b2) ...
+Removing debhelper (9.20160403) ...
+Removing dh-strip-nondeterminism (0.016-1) ...
+Removing man-db (2.7.5-1) ...
+Purging configuration files for man-db (2.7.5-1) ...
+Removing bsdmainutils (9.0.10) ...
+Purging configuration files for bsdmainutils (9.0.10) ...
+Removing po-debconf (1.0.19) ...
+Removing intltool-debian (0.35.0+20060710.4) ...
+Removing gettext (0.19.7-2) ...
+Removing gettext-base (0.19.7-2) ...
+Removing groff-base (1.22.3-7) ...
+Purging configuration files for groff-base (1.22.3-7) ...
+Removing libfile-stripnondeterminism-perl (0.016-1) ...
+Removing libarchive-zip-perl (1.57-1) ...
+Removing libbsd0:x32 (0.8.3-1) ...
+Removing libcroco3:x32 (0.6.11-1) ...
+Removing libglib2.0-0:x32 (2.48.0-1) ...
+Purging configuration files for libglib2.0-0:x32 (2.48.0-1) ...
+Removing libffi6:x32 (3.2.1-4) ...
+Removing libxml2:x32 (2.9.3+dfsg1-1) ...
+Removing libicu55:x32 (55.1-7) ...
+Removing libpipeline1:x32 (1.4.1-2) ...
+Removing libtimedate-perl (2.3000-2) ...
+Removing libunistring0:x32 (0.9.3-5.2) ...
+Purging configuration files for libunistring0:x32 (0.9.3-5.2) ...
+Removing dh-autoreconf (12) ...
+Removing automake (1:1.15-4) ...
+Removing autoconf (2.69-10) ...
+Purging configuration files for autoconf (2.69-10) ...
+Removing autopoint (0.19.7-2) ...
+Removing libtool (2.4.6-0.1) ...
+Removing autotools-dev (20150820.1) ...
+Removing file (1:5.25-2) ...
+Removing libmagic1:x32 (1:5.25-2) ...
+Purging configuration files for libmagic1:x32 (1:5.25-2) ...
+Removing m4 (1.4.17-5) ...
+Removing libsigsegv2:x32 (2.10-5) ...
+Processing triggers for libc-bin (2.22-7) ...
+W: No sandbox user '_apt' on the system, can not drop privileges
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: x32
-Build-Space: 16392
-Build-Time: 40
+Build-Space: 16736
+Build-Time: 113
Distribution: sid
Host Architecture: x32
-Install-Time: 11
-Job: samtools_1.3-1
+Install-Time: 37
+Job: samtools_1.3.1-1
Machine Architecture: amd64
Package: samtools
-Package-Time: 70
-Source-Version: 1.3-1
-Space: 16392
+Package-Time: 154
+Source-Version: 1.3.1-1
+Space: 16736
Status: successful
-Version: 1.3-1
+Version: 1.3.1-1
────────────────────────────────────────────────────────────────────────────────
-Finished at 20160205-1746
-Build needed 00:01:10, 16392k disc space
+Finished at 20160426-2309
+Build needed 00:02:34, 16736k disc space
Signature with key 'A644D214' requested:
- signfile /var/lib/buildd/build/samtools_1.3-1_x32.changes A644D214
+ signfile /var/lib/buildd/build/samtools_1.3.1-1_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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