[med-svn] samtools 01/04: Build logs for version 1.2-3.
Charles Plessy
plessy at moszumanska.debian.org
Wed Apr 27 00:55:14 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 c59f9c0335b6556d3c2a088f1086fc04dd4322ce
Author: Charles Plessy <plessy at debian.org>
Date: Wed Apr 27 09:49:36 2016 +0900
Build logs for version 1.2-3.
---
amd64.log | 2111 ------------------------------------
arm64.log | 1738 ++++++++++++++++++++++++-----
armel.log | 1732 +++++++++++++++++++++++++++++
armhf.log | 898 ---------------
hurd-i386.log | 973 -----------------
i386.log | 1695 +++++++++++++----------------
ia64.log | 958 ----------------
kfreebsd-amd64.log | 954 ++++++++--------
kfreebsd-i386.log | 1686 +++++++++++++---------------
mips.log | 1830 -------------------------------
kfreebsd-amd64.log => mips64el.log | 1087 ++++++++-----------
mipsel.log | 1787 ++++++++++++++----------------
powerpc.log | 899 ---------------
ppc64el.log | 1746 ++++++++++++++++++++++++-----
s390.log | 1798 ------------------------------
s390x.log | 905 ----------------
sparc.log | 610 -----------
x32.log | 768 +++++++++++++
18 files changed, 8714 insertions(+), 15461 deletions(-)
diff --git a/amd64.log b/amd64.log
deleted file mode 100644
index 9db22ca..0000000
--- a/amd64.log
+++ /dev/null
@@ -1,2111 +0,0 @@
-sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bubu.igloo
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.2-2 (amd64) 17 sept. 2015 20:23 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 1.2-2
-Source Version: 1.2-2
-Distribution: unstable
-Machine Architecture: amd64
-Host Architecture: amd64
-Build Architecture: amd64
-
-I: NOTICE: Log filtering will replace 'build/samtools-Ii1pvw/samtools-1.2' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-Ii1pvw' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-amd64-sbuild-de96647b-ea47-4cc5-9307-b2629755ee00' with '«CHROOT»'
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Update chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Hit http://ftp2.jp.debian.org sid InRelease
-Get:1 http://ftp2.jp.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:2 http://ftp2.jp.debian.org sid/main amd64 Packages/DiffIndex [7876 B]
-Get:3 http://ftp2.jp.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Fetched 23.6 kB in 1s (14.6 kB/s)
-Reading package lists...
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Local sources
-─────────────
-
-samtools_1.2-2.dsc exists in .; copying to chroot
-
-Check architectures
-───────────────────
-
-
-Check dependencies
-──────────────────
-
-Merged Build-Depends: build-essential, fakeroot
-Filtered Build-Depends: build-essential, fakeroot
-dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-82t7xC/apt_archive/sbuild-build-depends-core-dummy.deb'.
-OK
-Ign file: ./ InRelease
-Get:1 file: ./ Release.gpg [299 B]
-Get:2 file: ./ Release [2119 B]
-Ign file: ./ Translation-en
-Reading package lists...
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (apt-based resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Installing build dependencies
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following NEW packages will be installed:
- sbuild-build-depends-core-dummy
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
-Need to get 0 B/776 B of archives.
-After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ...
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(Reading database ... 11894 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-rMzyPf/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
-OK
-Ign file: ./ InRelease
-Get:1 file: ./ Release.gpg [299 B]
-Get:2 file: ./ Release [2119 B]
-Ign file: ./ Translation-en
-Reading package lists...
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (apt-based resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Installing build dependencies
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
- libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
-Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc autopoint
- libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
- libmail-box-perl
-Recommended packages:
- curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
- libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
- libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
- libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
- tabix zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded.
-Need to get 12.5 MB/18.3 MB of archives.
-After this operation, 65.3 MB of additional disk space will be used.
-Get:1 http://ftp2.jp.debian.org/debian/ sid/main bash-completion all 1:2.1-4.2 [179 kB]
-Get:2 http://ftp2.jp.debian.org/debian/ sid/main man-db amd64 2.7.3-1 [1001 kB]
-Get:3 http://ftp2.jp.debian.org/debian/ sid/main libicu55 amd64 55.1-5 [7651 kB]
-Get:4 http://ftp2.jp.debian.org/debian/ sid/main libxml2 amd64 2.9.2+really2.9.1+dfsg1-0.2 [905 kB]
-Get:5 http://ftp2.jp.debian.org/debian/ sid/main libmagic1 amd64 1:5.24-2 [255 kB]
-Get:6 http://ftp2.jp.debian.org/debian/ sid/main file amd64 1:5.24-2 [61.2 kB]
-Get:7 http://ftp2.jp.debian.org/debian/ sid/main gettext-base amd64 0.19.6-1 [123 kB]
-Get:8 http://ftp2.jp.debian.org/debian/ sid/main gettext amd64 0.19.6-1 [1468 kB]
-Get:9 http://ftp2.jp.debian.org/debian/ sid/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
-Get:10 http://ftp2.jp.debian.org/debian/ sid/main libhts-dev amd64 1.2.1-1 [278 kB]
-Get:11 http://ftp2.jp.debian.org/debian/ sid/main libio-pty-perl amd64 1:1.08-1+b4 [35.8 kB]
-Get:12 http://ftp2.jp.debian.org/debian/ sid/main libtinfo-dev amd64 6.0+20150810-1 [77.5 kB]
-Get:13 http://ftp2.jp.debian.org/debian/ sid/main libncurses5-dev amd64 6.0+20150810-1 [172 kB]
-Get:14 http://ftp2.jp.debian.org/debian/ sid/main tabix amd64 1.2.1-1 [223 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 12.5 MB in 12s (971 kB/s)
-Selecting previously unselected package bash-completion.
-(Reading database ...
(Reading database ... 5%
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(Reading database ... 11894 files and directories currently installed.)
-Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
-Unpacking bash-completion (1:2.1-4.2) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.3-1_amd64.deb ...
-Unpacking groff-base (1.22.3-1) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.6_amd64.deb ...
-Unpacking bsdmainutils (9.0.6) ...
-Selecting previously unselected package libpipeline1:amd64.
-Preparing to unpack .../libpipeline1_1.4.1-1_amd64.deb ...
-Unpacking libpipeline1:amd64 (1.4.1-1) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.3-1_amd64.deb ...
-Unpacking man-db (2.7.3-1) ...
-Selecting previously unselected package libffi6:amd64.
-Preparing to unpack .../libffi6_3.2.1-3_amd64.deb ...
-Unpacking libffi6:amd64 (3.2.1-3) ...
-Selecting previously unselected package libglib2.0-0:amd64.
-Preparing to unpack .../libglib2.0-0_2.44.1-1.1_amd64.deb ...
-Unpacking libglib2.0-0:amd64 (2.44.1-1.1) ...
-Selecting previously unselected package libicu55:amd64.
-Preparing to unpack .../libicu55_55.1-5_amd64.deb ...
-Unpacking libicu55:amd64 (55.1-5) ...
-Selecting previously unselected package libxml2:amd64.
-Preparing to unpack .../libxml2_2.9.2+really2.9.1+dfsg1-0.2_amd64.deb ...
-Unpacking libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
-Selecting previously unselected package libcroco3:amd64.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_amd64.deb ...
-Unpacking libcroco3:amd64 (0.6.8-3+b1) ...
-Selecting previously unselected package libunistring0:amd64.
-Preparing to unpack .../libunistring0_0.9.3-5.2+b1_amd64.deb ...
-Unpacking libunistring0:amd64 (0.9.3-5.2+b1) ...
-Selecting previously unselected package libmagic1:amd64.
-Preparing to unpack .../libmagic1_1%3a5.24-2_amd64.deb ...
-Unpacking libmagic1:amd64 (1:5.24-2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.24-2_amd64.deb ...
-Unpacking file (1:5.24-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.6-1_amd64.deb ...
-Unpacking gettext-base (0.19.6-1) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.6-1_amd64.deb ...
-Unpacking gettext (0.19.6-1) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.4) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.18_all.deb ...
-Unpacking po-debconf (1.0.18) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20150811_all.deb ...
-Unpacking debhelper (9.20150811) ...
-Selecting previously unselected package libhts1:amd64.
-Preparing to unpack .../libhts1_1.2.1-1_amd64.deb ...
-Unpacking libhts1:amd64 (1.2.1-1) ...
-Selecting previously unselected package libhts-dev:amd64.
-Preparing to unpack .../libhts-dev_1.2.1-1_amd64.deb ...
-Unpacking libhts-dev:amd64 (1.2.1-1) ...
-Selecting previously unselected package libio-pty-perl.
-Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_amd64.deb ...
-Unpacking libio-pty-perl (1:1.08-1+b4) ...
-Selecting previously unselected package libtinfo-dev:amd64.
-Preparing to unpack .../libtinfo-dev_6.0+20150810-1_amd64.deb ...
-Unpacking libtinfo-dev:amd64 (6.0+20150810-1) ...
-Selecting previously unselected package libncurses5-dev:amd64.
-Preparing to unpack .../libncurses5-dev_6.0+20150810-1_amd64.deb ...
-Unpacking libncurses5-dev:amd64 (6.0+20150810-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.2.1-1_amd64.deb ...
-Unpacking tabix (1.2.1-1) ...
-Selecting previously unselected package zlib1g-dev:amd64.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_amd64.deb ...
-Unpacking zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up bash-completion (1:2.1-4.2) ...
-Setting up groff-base (1.22.3-1) ...
-Setting up bsdmainutils (9.0.6) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up libpipeline1:amd64 (1.4.1-1) ...
-Setting up man-db (2.7.3-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up libffi6:amd64 (3.2.1-3) ...
-Setting up libglib2.0-0:amd64 (2.44.1-1.1) ...
-No schema files found: doing nothing.
-Setting up libicu55:amd64 (55.1-5) ...
-Setting up libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
-Setting up libcroco3:amd64 (0.6.8-3+b1) ...
-Setting up libunistring0:amd64 (0.9.3-5.2+b1) ...
-Setting up libmagic1:amd64 (1:5.24-2) ...
-Setting up file (1:5.24-2) ...
-Setting up gettext-base (0.19.6-1) ...
-Setting up gettext (0.19.6-1) ...
-Setting up intltool-debian (0.35.0+20060710.4) ...
-Setting up po-debconf (1.0.18) ...
-Setting up debhelper (9.20150811) ...
-Setting up libhts1:amd64 (1.2.1-1) ...
-Setting up libhts-dev:amd64 (1.2.1-1) ...
-Setting up libio-pty-perl (1:1.08-1+b4) ...
-Setting up libtinfo-dev:amd64 (6.0+20150810-1) ...
-Setting up libncurses5-dev:amd64 (6.0+20150810-1) ...
-Setting up tabix (1.2.1-1) ...
-Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-20) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build environment │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Kernel: Linux 4.1.0-0.bpo.2-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
-Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debfoster_2.7-2 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-dpkg-source: warning: extracting unsigned source package (samtools_1.2-2.dsc)
-dpkg-source: info: extracting samtools in samtools-1.2
-dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.2-2.debian.tar.xz
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying i386-build.patch
-
-Check disc space
-────────────────
-
-Sufficient free space for build
-
-User Environment
-────────────────
-
-HOME=/sbuild-nonexistent
-LD_LIBRARY_PATH=/usr/lib/libeatmydata
-LD_PRELOAD=libeatmydata.so
-LOGNAME=charles
-PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-PWD=/«PKGBUILDDIR»
-SCHROOT_ALIAS_NAME=unstable
-SCHROOT_CHROOT_NAME=sid-amd64-sbuild
-SCHROOT_COMMAND=env
-SCHROOT_GID=1000
-SCHROOT_GROUP=charles
-SCHROOT_SESSION_ID=sid-amd64-sbuild-de96647b-ea47-4cc5-9307-b2629755ee00
-SCHROOT_UID=1000
-SCHROOT_USER=charles
-SHELL=/bin/sh
-TERM=xterm
-USER=charles
-USERNAME=charles
-XDG_RUNTIME_DIR=/run/user/1000
-XDG_SEAT=seat0
-XDG_SESSION_ID=1
-XDG_VTNR=7
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.2-2
-dpkg-buildpackage: source distribution unstable
-dpkg-buildpackage: source changed by Charles Plessy <plessy at debian.org>
- dpkg-source --before-build samtools-1.2
-dpkg-buildpackage: host architecture amd64
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
- fakeroot debian/rules clean
-dh clean --parallel
- dh_testdir
- dh_auto_clean
- make -j1 distclean
-make[1]: Entering directory '/«PKGBUILDDIR»'
-rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
-cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
-rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
-rm -f TAGS
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- dh_clean
- 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
- dpkg-source -b samtools-1.2
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
-dpkg-source: info: using source format '3.0 (quilt)'
-dpkg-source: info: building samtools using existing ./samtools_1.2.orig.tar.gz
-dpkg-source: info: building samtools in samtools_1.2-2.debian.tar.xz
-dpkg-source: info: building samtools in samtools_1.2-2.dsc
- debian/rules build
-dh build --parallel
- dh_testdir
- dh_auto_configure
- debian/rules override_dh_auto_build
-make[1]: Entering directory '/«PKGBUILDDIR»'
-dh_auto_build -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a \
- CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
- CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
- LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
- LDLIBS="-lhts"
- make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
-make[2]: Entering directory '/«PKGBUILDDIR»'
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.2"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
-ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
-ar: `u' modifier ignored since `D' is the default (see `U')
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lcurses -lm -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
-gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
-gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
-gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
-gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
-gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
-gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
-gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
-gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
-gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-linux-gnu/libhts.a -lhts -lz
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- debian/rules override_dh_auto_test
-make[1]: Entering directory '/«PKGBUILDDIR»'
-dh_auto_test -- \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a \
- BGZIP=/usr/bin/bgzip
- make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
-make[2]: Entering directory '/«PKGBUILDDIR»'
-REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/FL8pW6xlSN/bgzip.dat.gz
-.. ok
-
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/FL8pW6xlSN/bgzip.dat.gz
-.. ok
-
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/FL8pW6xlSN/bgzip.dat.gz
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 3:11-13 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 3:11-13 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 2:998-1003 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 2:998-1003 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 1:100-104 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 1:100-104 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa 1:99998-100007 | grep -v '^>'
-.. ok
-
-/«PKGBUILDDIR»/samtools faidx /tmp/FL8pW6xlSN/faidx.fa.gz 1:99998-100007 | grep -v '^>'
-.. ok
-
-test_index:
- /«PKGBUILDDIR»/samtools index /tmp/FL8pW6xlSN/large_chrom.bam
-
-.. expected failure
-
-test_index:
- /«PKGBUILDDIR»/samtools view /tmp/FL8pW6xlSN/large_chrom.bam ref2
-.. ok
-
-test_index:
- /«PKGBUILDDIR»/samtools view /tmp/FL8pW6xlSN/large_chrom.bam ref2:1-541556283
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/FL8pW6xlSN/mpileup.bam.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-150
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-150
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/FL8pW6xlSN/mpileup.bam.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/FL8pW6xlSN/mpileup.cram.list -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:1050-1060 /tmp/FL8pW6xlSN/mpileup.1.bam | grep -v mpileup
-.. ok
-
-test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/FL8pW6xlSN/mpileup.ref.fa.gz -r17:1050-1060 /tmp/FL8pW6xlSN/mpileup.1.cram | grep -v mpileup
-.. ok
-
-test_usage:
- samtools
- samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
-.. ok
-
-test_usage_subcommand:
- samtools faidx
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools index
-.. ok
-
-test_usage_subcommand:
- samtools calmd
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools fixmate
-.. ok
-
-test_usage_subcommand:
- samtools reheader
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools rmdup
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools targetcut
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools bamshuf
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools cat
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools merge
-.. ok
-
-test_usage_subcommand:
- samtools mpileup
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools sort
-.. ok
-
-test_usage_subcommand:
- samtools split
-.. ok
-
-test_usage_subcommand:
- samtools bam2fq
-.. ok
-
-test_usage_subcommand:
- samtools bedcov
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools depth
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools flagstat
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools idxstats
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools phase
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools stats
-.. ok
-
-test_usage_subcommand:
- samtools flags
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools tview
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_usage_subcommand:
- samtools view
-
- Usage on stderr rather than stdout
-.. expected failure
-
-test_view:
- Generating test data file .................. done
- 1: SAM -> BAM -> SAM .. ok
-
- 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/FL8pW6xlSN/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input) .. ok
-
- 52: Count -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input) .. ok
-
- 53: Filter -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input) .. ok
-
- 54: Count -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input) .. ok
-
- 55: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (SAM input).. ok
-
- 56: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (SAM input).. ok
-
- 57: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (BAM input).. ok
-
- 58: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (BAM input).. ok
-
- 59: Filter -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (CRAM input).. ok
-
- 60: Count -R /tmp/FL8pW6xlSN/view.001.fogn -r grp2 (CRAM input).. ok
-
- 61: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input).. ok
-
- 62: Count -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (SAM input).. ok
-
- 63: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input).. ok
-
- 64: Count -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (BAM input).. ok
-
- 65: Filter -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input).. ok
-
- 66: Count -r grp2 -R /tmp/FL8pW6xlSN/view.001.fogn (CRAM input).. ok
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test067.sam -h -l Library 2 /tmp/FL8pW6xlSN/view.001.sam
-
-
-.. expected failure
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/view.001.sam
-
-
-.. expected failure
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test069.sam -h -l Library 2 /tmp/FL8pW6xlSN/view.test001.bam
-
-
-.. expected failure
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/view.test001.bam
-
-
-.. expected failure
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/FL8pW6xlSN/view.test071.sam -h -l Library 2 /tmp/FL8pW6xlSN/view.test006.cram
-
-
-.. expected failure
-
-Samtools-htslib-API: bam_get_library() not yet implemented
- 72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/FL8pW6xlSN/view.test006.cram
-
-
-.. expected failure
-
- 73: Filter -q 50 (SAM input) .. ok
-
- 74: Count -q 50 (SAM input) .. ok
-
- 75: Filter -q 50 (BAM input) .. ok
-
- 76: Count -q 50 (BAM input) .. ok
-
- 77: Filter -q 50 (CRAM input) .. ok
-
- 78: Count -q 50 (CRAM input) .. ok
-
- 79: Filter -q 99 (SAM input) .. ok
-
- 80: Count -q 99 (SAM input) .. ok
-
- 81: Filter -q 99 (BAM input) .. ok
-
- 82: Count -q 99 (BAM input) .. ok
-
- 83: Filter -q 99 (CRAM input) .. ok
-
- 84: Count -q 99 (CRAM input) .. ok
-
- 85: Filter -q 100 (SAM input) .. ok
-
- 86: Count -q 100 (SAM input) .. ok
-
- 87: Filter -q 100 (BAM input) .. ok
-
- 88: Count -q 100 (BAM input) .. ok
-
- 89: Filter -q 100 (CRAM input) .. ok
-
- 90: Count -q 100 (CRAM input) .. ok
-
- 91: Filter -x fa (SAM input) .. ok
-
- 92: Count -x fa (SAM input) .. ok
-
- 93: Filter -x fa (BAM input) .. ok
-
- 94: Count -x fa (BAM input) .. ok
-
- 95: Filter -x fa (CRAM input) .. ok
-
- 96: Count -x fa (CRAM input) .. ok
-
- 97: Filter -x fa -x ha (SAM input) .. ok
-
- 98: Count -x fa -x ha (SAM input) .. ok
-
- 99: Filter -x fa -x ha (BAM input) .. ok
-
- 100: Count -x fa -x ha (BAM input) .. ok
-
- 101: Filter -x fa -x ha (CRAM input) .. ok
-
- 102: Count -x fa -x ha (CRAM input) .. ok
-
- 103: Filter -x fa -r grp2 (SAM input) .. ok
-
- 104: Count -x fa -r grp2 (SAM input) .. ok
-
- 105: Filter -x fa -r grp2 (BAM input) .. ok
-
- 106: Count -x fa -r grp2 (BAM input) .. ok
-
- 107: Filter -x fa -r grp2 (CRAM input) .. ok
-
- 108: Count -x fa -r grp2 (CRAM input) .. ok
-
- 109: Filter -x RG -r grp2 (SAM input) .. ok
-
- 110: Count -x RG -r grp2 (SAM input) .. ok
-
- 111: Filter -x RG -r grp2 (BAM input) .. ok
-
- 112: Count -x RG -r grp2 (BAM input) .. ok
-
- 113: Filter -x RG -r grp2 (CRAM input) .. ok
-
- 114: Count -x RG -r grp2 (CRAM input) .. ok
-
- 115: Filter -m 10 (SAM input) .. ok
-
- 116: Count -m 10 (SAM input) .. ok
-
- 117: Filter -m 10 (BAM input) .. ok
-
- 118: Count -m 10 (BAM input) .. ok
-
- 119: Filter -m 10 (CRAM input) .. ok
-
- 120: Count -m 10 (CRAM input) .. ok
-
- 121: Filter -m 11 (SAM input) .. ok
-
- 122: Count -m 11 (SAM input) .. ok
-
- 123: Filter -m 11 (BAM input) .. ok
-
- 124: Count -m 11 (BAM input) .. ok
-
- 125: Filter -m 11 (CRAM input) .. ok
-
- 126: Count -m 11 (CRAM input) .. ok
-
- 127: Filter -m 15 (SAM input) .. ok
-
- 128: Count -m 15 (SAM input) .. ok
-
- 129: Filter -m 15 (BAM input) .. ok
-
- 130: Count -m 15 (BAM input) .. ok
-
- 131: Filter -m 15 (CRAM input) .. ok
-
- 132: Count -m 15 (CRAM input) .. ok
-
- 133: Filter -m 16 (SAM input) .. ok
-
- 134: Count -m 16 (SAM input) .. ok
-
- 135: Filter -m 16 (BAM input) .. ok
-
- 136: Count -m 16 (BAM input) .. ok
-
- 137: Filter -m 16 (CRAM input) .. ok
-
- 138: Count -m 16 (CRAM input) .. ok
-
- 139: 1bp reads file SAM -> BAM -> SAM .. ok
-
- 140: 1bp reads file SAM -> CRAM -> SAM .. ok
-
- 140: Region Z (BAM input) .. ok
-
- 141: Count Z (BAM input) .. ok
-
- 142: Region Z (CRAM input) .. ok
-
- 143: Count Z (CRAM input) .. ok
-
- 144: Region Z:30 (BAM input) .. ok
-
- 145: Count Z:30 (BAM input) .. ok
-
- 146: Region Z:30 (CRAM input) .. ok
-
- 147: Count Z:30 (CRAM input) .. ok
-
- 148: Region Z:20-40 (BAM input) .. ok
-
- 149: Count Z:20-40 (BAM input) .. ok
-
- 150: Region Z:20-40 (CRAM input) .. ok
-
- 151: Count Z:20-40 (CRAM input) .. ok
-
- 152: Region ref1 (BAM input) .. ok
-
- 153: Count ref1 (BAM input) .. ok
-
- 154: Region ref1 (CRAM input) .. ok
-
- 155: Count ref1 (CRAM input) .. ok
-
- 156: Region ref1:15 (BAM input) .. ok
-
- 157: Count ref1:15 (BAM input) .. ok
-
- 158: Region ref1:15 (CRAM input) .. ok
-
- 159: Count ref1:15 (CRAM input) .. ok
-
- 160: Region ref1:15-45 (BAM input) .. ok
-
- 161: Count ref1:15-45 (BAM input) .. ok
-
- 162: Region ref1:15-45 (CRAM input) .. ok
-
- 163: Count ref1:15-45 (CRAM input) .. ok
-
- 164: Region ref1:15-45 ref2 (BAM input) .. ok
-
- 165: Count ref1:15-45 ref2 (BAM input) .. ok
-
- 166: Region ref1:15-45 ref2 (CRAM input) .. ok
-
- 167: Count ref1:15-45 ref2 (CRAM input) .. ok
-
- 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
-
- 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
-
- 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
-
- 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
-
- 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
-
- 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
-
- 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
-
- 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
-
- 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
-
- 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
-
- 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
-
- 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
-
- 180: Region -f 128 ref1 (BAM input) .. ok
-
- 181: Count -f 128 ref1 (BAM input) .. ok
-
- 182: Region -f 128 ref1 (CRAM input) .. ok
-
- 183: Count -f 128 ref1 (CRAM input) .. ok
-
- 184: Region -q 50 ref1:15-45 (BAM input) .. ok
-
- 185: Count -q 50 ref1:15-45 (BAM input) .. ok
-
- 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
-
- 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
-
- 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
-
- 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
-
- 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
-
- 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
-
- 192: 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
-
- 194: 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
-
- 196: 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
-
- 198: 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
-
- 200: 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
-
- 202: 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
-
- 204: 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
-
- 206: 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
-
- 208: 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
-
- 210: 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
-
- 212: 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
-
- 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:30 (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:10-30 (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:10-30 (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:25-35 (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:25-35 (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.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
-
- 227: 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
-
- 229: 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
-
- 231: 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
-
- 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 -r grp1 (CRAM 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 -f 128 (BAM 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 -f 128 (CRAM 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 -q 5 (BAM 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 -q 5 (CRAM 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 -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
-
- 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 -r grp1 ref1:11-16 (CRAM input).. ok
-
- 248: Make BAM with no M5/UR tags .. ok
-
- 249: Add @SQ with -t (SAM -> SAM) .. ok
-
- 250: Add @SQ with -T (SAM -> SAM) .. ok
-
- 251: Add @SQ with -t (BAM -> SAM) .. ok
-
- 252: Add @SQ with -T (BAM -> SAM) .. ok
-
- 253: Add @SQ with -t (SAM -> BAM) .. ok
-
- 254: Add @SQ with -T (SAM -> BAM) .. ok
-
- 255: Add @SQ with -t (BAM -> BAM) .. ok
-
- 256: Add @SQ with -T (BAM -> BAM) .. ok
-
- 257: Add @SQ with -t (SAM -> CRAM) .. ok
-
- 258: Add @SQ with -T (SAM -> CRAM) .. ok
-
- 259: Add @SQ with -t (BAM -> CRAM) .. ok
-
- 260: Add @SQ with -T (BAM -> CRAM) .. ok
-
- 261: Make CRAM with no UR field .. ok
-
- 262: Decoding CRAM with no UR field via -T .. ok
-
- 263: CIGAR B-operator removal .. ok
-
- 264: Big SAM -> BAM .. ok
-
- 265: Big SAM -> BAM (2 threads) .. ok
-
- 266: Big SAM -> BAM (4 threads) .. ok
-
- 267: Big SAM -> CRAM .. ok
-
- 268: Big SAM -> CRAM (2 threads) .. ok
-
- 269: Big SAM -> CRAM (4 threads) .. ok
-
- 270: Subsample 0.2 (SAM input) ............ ok
-
- 271: Subsample 0.5 (SAM input) ............ ok
-
- 272: Subsample 0.8 (SAM input) ............ ok
-
- 273: Subsample 0.2 (BAM input) ............ ok
-
- 274: Subsample 0.5 (BAM input) ............ ok
-
- 275: Subsample 0.8 (BAM input) ............ ok
-
- 276: Subsample 0.2 (CRAM input) ............ ok
-
- 277: Subsample 0.5 (CRAM input) ............ ok
-
- 278: Subsample 0.8 (CRAM input) ............ ok
-
-test_cat:
- Generating test data file .................. done
- Generate BAM file #1 .. ok
-
- Generating test data file .................. done
- Generate BAM file #2 .. ok
-
- Generating test data file .................. done
- Generate BAM file #3 .. ok
-
- Generating test data file .................. done
- Generate BAM file #4 .. ok
-
- 1: cat BAM files .. ok
-
- 2: cat recompressed BAM files .. ok
-
- 3: cat BAM files to stdout .. ok
-
- 4: cat recompressed BAM files to stdout .. ok
-
- 5: cat BAM files with new header .. ok
-
- 6: cat recompressed BAM files with new header .. ok
-
-test_bam2fq:
- Generate BAM file .. ok
-
-Unsorted mode enabled
- Generate CRAM file .. ok
-
-[M::main_bam2fq] processed 36 reads
- 1: bam2fq (SAM input) .. ok
-
-[M::main_bam2fq] processed 36 reads
- 2: bam2fq -n (SAM input) .. ok
-
-[M::main_bam2fq] processed 36 reads
- 3: bam2fq (BAM input) .. ok
-
-[M::main_bam2fq] processed 36 reads
- 4: bam2fq -n (BAM input) .. ok
-
-[M::main_bam2fq] processed 36 reads
- 5: bam2fq (CRAM input) .. ok
-
-[M::main_bam2fq] processed 36 reads
- 6: bam2fq -n (CRAM input) .. ok
-
-test_depad:
- Generate BAM file .. ok
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/FL8pW6xlSN/depad.001p.bam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/FL8pW6xlSN/depad.001p.bam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/FL8pW6xlSN/depad.001p.bam
-
-
-.. expected failure
-
-Samtools-htslib: fix_header() header parsing not yet implemented
- depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/FL8pW6xlSN/depad.001p.bam
-
-
-.. expected failure
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
-.. ok
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
-.. ok
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
-.. ok
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
-.. ok
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
-.. ok
-
-test_stats:
- /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
-.. 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/zC4zgzSqm5 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
-.. ok
-
-test_fixmate:
- /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
-
-.. 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
-
-test_idxstat:
- /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
-.. ok
-
-
-Number of tests:
- total .. 368
- passed .. 336
- failed .. 0
- expected failure .. 32
- unexpected pass .. 0
-
-test/merge/test_bam_translate test/merge/test_bam_translate.tmp
-test/merge/test_pretty_header
-test/merge/test_rtrans_build
-test/merge/test_trans_tbl_init
-cd test/mpileup && ./regression.sh
-Samtools mpileup tests:
-
-EXPECTED FAIL: Task failed, but expected to fail;
-when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
-
-Expected passes: 123
-Unexpected passes: 0
-Expected failures: 1
-Unexpected failures: 0
-=> PASS
-test/split/test_count_rg
-test/split/test_expand_format_string
-test/split/test_filter_header_rg
-test/split/test_parse_args
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- fakeroot debian/rules binary
-dh binary --parallel
- dh_testroot
- dh_prep
- 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/
- debian/rules override_dh_auto_install
-make[1]: Entering directory '/«PKGBUILDDIR»'
-dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a
- install -d debian/samtools
- install -d debian/samtools-test
- make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnu/libhts.a
-make[2]: Entering directory '/«PKGBUILDDIR»'
-mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
-install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
-install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make clean
-make[2]: Entering directory '/«PKGBUILDDIR»'
-rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
-cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
-rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-for script in /«PKGBUILDDIR»/debian/tmp/usr/bin/*.*; \
-do \
- mv $script ${script%.*}; \
- ln -s `basename ${script%.*}` $script; \
-done
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- dh_install
- install -d debian/samtools//usr
- cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
- install -d debian/samtools//usr/share/man
- cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
- install -d debian/samtools-test/usr/share/samtools
- cp --reflink=auto -a ./test debian/samtools-test/usr/share/samtools/
- dh_installdocs
- 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
- 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
- install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
- install -p -m0644 debian/changelog debian/samtools-test/usr/share/doc/samtools-test/changelog.Debian
- dh_installman
- man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
- chmod 644 samtools.1.new
- mv -f samtools.1.new samtools.1
- dh_perl
- (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
- mv debian/samtools.substvars.new debian/samtools.substvars
- (grep -s -v perl:Depends debian/samtools-test.substvars; echo perl:Depends=perl) > debian/samtools-test.substvars.new
- mv debian/samtools-test.substvars.new debian/samtools-test.substvars
- dh_link
- rm -f debian/samtools/usr/bin/interpolate_sam.pl
- ln -sf interpolate_sam debian/samtools/usr/bin/interpolate_sam.pl
- rm -f debian/samtools/usr/bin/bowtie2sam.pl
- ln -sf bowtie2sam debian/samtools/usr/bin/bowtie2sam.pl
- rm -f debian/samtools/usr/bin/export2sam.pl
- ln -sf export2sam debian/samtools/usr/bin/export2sam.pl
- rm -f debian/samtools/usr/bin/sam2vcf.pl
- ln -sf sam2vcf debian/samtools/usr/bin/sam2vcf.pl
- rm -f debian/samtools/usr/bin/soap2sam.pl
- ln -sf soap2sam debian/samtools/usr/bin/soap2sam.pl
- rm -f debian/samtools/usr/bin/novo2sam.pl
- ln -sf novo2sam debian/samtools/usr/bin/novo2sam.pl
- rm -f debian/samtools/usr/bin/blast2sam.pl
- ln -sf blast2sam debian/samtools/usr/bin/blast2sam.pl
- rm -f debian/samtools/usr/bin/psl2sam.pl
- ln -sf psl2sam debian/samtools/usr/bin/psl2sam.pl
- rm -f debian/samtools/usr/bin/samtools.pl
- ln -sf samtools debian/samtools/usr/bin/samtools.pl
- rm -f debian/samtools/usr/bin/wgsim_eval.pl
- ln -sf wgsim_eval debian/samtools/usr/bin/wgsim_eval.pl
- rm -f debian/samtools/usr/bin/zoom2sam.pl
- ln -sf zoom2sam debian/samtools/usr/bin/zoom2sam.pl
- rm -f debian/samtools/usr/bin/varfilter.py
- ln -sf varfilter debian/samtools/usr/bin/varfilter.py
- rm -f debian/samtools/usr/bin/seq_cache_populate.pl
- ln -sf seq_cache_populate debian/samtools/usr/bin/seq_cache_populate.pl
- dh_compress
- cd debian/samtools
- chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
- gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
- cd '/«PKGBUILDDIR»'
- cd debian/samtools-test
- chmod a-x usr/share/doc/samtools-test/changelog.Debian
- gzip -9nf usr/share/doc/samtools-test/changelog.Debian
- cd '/«PKGBUILDDIR»'
- dh_fixperms
- find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
- find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
- find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
- find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
- find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
- find debian/samtools-test -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
- find debian/samtools-test ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
- find debian/samtools-test/usr/share/doc -type f ! -regex 'debian/samtools-test/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
- find debian/samtools-test/usr/share/man debian/samtools-test/usr/man/ debian/samtools-test/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
- find debian/samtools-test/usr/lib/x86_64-linux-gnu/perl5/5.20 debian/samtools-test/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
- find debian/samtools-test/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
- dh_strip
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
- dh_makeshlibs
- rm -f debian/samtools/DEBIAN/shlibs
- rm -f debian/samtools-test/DEBIAN/shlibs
- dh_shlibdeps
- install -d debian/samtools/DEBIAN
- dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short
-dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
- install -d debian/samtools-test/DEBIAN
- dh_installdeb
- dh_gencontrol
- echo misc:Depends= >> debian/samtools.substvars
- echo misc:Pre-Depends= >> debian/samtools.substvars
- dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
-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
- 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
- (cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
- chmod 0644 debian/samtools/DEBIAN/md5sums
- chown 0:0 debian/samtools/DEBIAN/md5sums
- (cd debian/samtools-test >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
- chmod 0644 debian/samtools-test/DEBIAN/md5sums
- chown 0:0 debian/samtools-test/DEBIAN/md5sums
- dh_builddeb
- dpkg-deb --build debian/samtools ..
-dpkg-deb: building package 'samtools' in '../samtools_1.2-2_amd64.deb'.
- dpkg-deb --build debian/samtools-test ..
-dpkg-deb: building package 'samtools-test' in '../samtools-test_1.2-2_all.deb'.
- dpkg-genchanges >../samtools_1.2-2_amd64.changes
-dpkg-genchanges: not including original source code in upload
- dpkg-source --after-build samtools-1.2
-dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
-dpkg-buildpackage: binary and diff upload (original source NOT included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20150917-2025
-
-Finished
-────────
-
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build Chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_1.2-2_amd64.changes:
-─────────────────────────────
-
-Format: 1.8
-Date: Thu, 17 Sep 2015 20:21:15 +0900
-Source: samtools
-Binary: samtools samtools-test
-Architecture: source all amd64
-Version: 1.2-2
-Distribution: unstable
-Urgency: medium
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.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 (1.2-2) unstable; urgency=medium
- .
- [ Afif Elghraoui ]
- eb56918 Add patch to fix building on i386
- 702d289 Remove source files not present in upstream tarball
- 7afd302 Allow all scripts to be called without language extensions
- .
- [ Charles Plessy ]
- 876f680 Document the update workflow of the source package's repository.
-Checksums-Sha1:
- a485f12b5d4ae124d677ef76e21219b3dbc81f1b 1248 samtools_1.2-2.dsc
- 67060d378093df98a1a5e579f8aa717f7d820ddb 9660 samtools_1.2-2.debian.tar.xz
- 42c12bab33f018b73d97617f54c6820a1fb32fa8 2646396 samtools-test_1.2-2_all.deb
- ceed8d67a37aef4352f4134fdabc585cbfa04a41 75450 samtools_1.2-2_amd64.deb
-Checksums-Sha256:
- 74d34f20c9e8d401ebf2ee028f81114618fcf353406afa40bca593bcbd6166cc 1248 samtools_1.2-2.dsc
- 45e989172a110c980a50380e13979eec78d982b75ddccae33f1c6f4e931ef686 9660 samtools_1.2-2.debian.tar.xz
- 8fc146560ecf3658e7287128ffc4f54c224f810c03e0a7565f0c3b595997ba12 2646396 samtools-test_1.2-2_all.deb
- 5228feb9b9d48c2ce843420266760c224e1e14758671b6c82e0c4009bc73a35f 75450 samtools_1.2-2_amd64.deb
-Files:
- bc235ec04c9c2d2016d5cfcb49d98ada 1248 science optional samtools_1.2-2.dsc
- 042d3648bfecb640ddca7a9ab34033c4 9660 science optional samtools_1.2-2.debian.tar.xz
- 19dc121013e77df2f8d64d5bb954031a 2646396 science optional samtools-test_1.2-2_all.deb
- 4c2ad525426b028fb47ea329de21da6c 75450 science optional samtools_1.2-2_amd64.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools-test_1.2-2_all.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 2646396 bytes: control archive=5623 bytes.
- 494 bytes, 15 lines control
- 17627 bytes, 215 lines md5sums
- Package: samtools-test
- Source: samtools
- Version: 1.2-2
- Architecture: all
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 9222
- Recommends: libio-pty-perl
- Section: science
- Priority: optional
- Homepage: http://www.htslib.org/
- Description: test files for the samtools package.
- Samtools is a set of utilities that manipulate nucleotide sequence alignments
- in the binary BAM format.
- .
- This package contains test files for the samtools package.
-
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/samtools-test/
--rw-r--r-- root/root 3542 2015-09-17 20:22 ./usr/share/doc/samtools-test/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-17 20:15 ./usr/share/doc/samtools-test/copyright
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/test/
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/
--rw-r--r-- root/root 5280 2015-02-03 00:18 ./usr/share/samtools/test/dat/bam2fq.001.sam
--rw-r--r-- root/root 1292 2015-02-03 00:18 ./usr/share/samtools/test/dat/cat.hdr
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/
--rw-r--r-- root/root 57 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/08c04d512d4797d9ba2a156c1daba468
--rw-r--r-- root/root 61 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/7c35feac7036c1cdef3bee0cc4b21437
--rw-r--r-- root/root 36 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/89b96de7acc5918c2858ef92710be7d4
--rw-r--r-- root/root 31 2015-02-03 00:18 ./usr/share/samtools/test/dat/cram_md5/8a3d8deb9edd4ce3346b6061fcee6d0b
--rw-r--r-- root/root 42 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001.fa
--rw-r--r-- root/root 16 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001.fa.fai
--rw-r--r-- root/root 7908 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001p.sam
--rw-r--r-- root/root 7914 2015-02-03 00:18 ./usr/share/samtools/test/dat/depad.001u.sam
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/dat/empty.expected
--rw-r--r-- root/root 624 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom.out
--rw-r--r-- root/root 5090 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom.sam
--rw-r--r-- root/root 92 2015-02-03 00:18 ./usr/share/samtools/test/dat/large_chrom_bai_index.err
--rw-r--r-- root/root 351091 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.1.sam
--rw-r--r-- root/root 104866 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.2.sam
--rw-r--r-- root/root 105843 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.3.sam
--rw-r--r-- root/root 78 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.err.1
--rw-r--r-- root/root 2716 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.1
--rw-r--r-- root/root 81484 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.2
--rw-r--r-- root/root 295 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.3
--rw-r--r-- root/root 113722 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.out.4
--rw-r--r-- root/root 4284 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.ref.fa
--rw-r--r-- root/root 17 2015-02-03 00:18 ./usr/share/samtools/test/dat/mpileup.ref.fa.fai
--rw-r--r-- root/root 758 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.bam
--rw-r--r-- root/root 264 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.bam.bai
--rw-r--r-- root/root 1429 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_a.sam
--rw-r--r-- root/root 687 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.bam
--rw-r--r-- root/root 192 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.bam.bai
--rw-r--r-- root/root 1252 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_b.sam
--rw-r--r-- root/root 655 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.bam
--rw-r--r-- root/root 176 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.bam.bai
--rw-r--r-- root/root 1253 2015-02-03 00:18 ./usr/share/samtools/test/dat/test_input_1_c.sam
--rw-r--r-- root/root 1335 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.01.bed
--rw-r--r-- root/root 1134 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.02.bed
--rw-r--r-- root/root 130 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.fa
--rw-r--r-- root/root 33 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.fa.fai
--rw-r--r-- root/root 5073 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.001.sam
--rw-r--r-- root/root 1313 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.01.bed
--rw-r--r-- root/root 1302 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.02.bed
--rw-r--r-- root/root 64 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.fa
--rw-r--r-- root/root 13 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.fa.fai
--rw-r--r-- root/root 3692 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.002.sam
--rw-r--r-- root/root 2142 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.003.expected.sam
--rw-r--r-- root/root 2224 2015-02-03 00:18 ./usr/share/samtools/test/dat/view.003.sam
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/
--rw-r--r-- root/root 894 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected
--rw-r--r-- root/root 82 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/1_coord_sort.sam.expected.err
--rw-r--r-- root/root 1047 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam
--rw-r--r-- root/root 1102 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/2_isize_overflow.sam.expected
--rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam
--rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/3_reverse_read_pp_lt.sam.expected
--rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam
--rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/4_reverse_read_pp_equal.sam.expected
--rw-r--r-- root/root 715 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/5_ct.sam
--rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/5_ct.sam.expected
--rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/6_ct_replace.sam
--rw-r--r-- root/root 735 2015-02-03 00:18 ./usr/share/samtools/test/fixmate/6_ct_replace.sam.expected
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/
--rw-r--r-- root/root 58 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/idxstats/test_input_1_a.bam.expected.err
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/test/merge/
--rw-r--r-- root/root 1181 2015-02-03 00:18 ./usr/share/samtools/test/merge/2.merge.expected.bam
--rw-r--r-- root/root 1199 2015-02-03 00:18 ./usr/share/samtools/test/merge/3.merge.expected.bam
--rw-r--r-- root/root 525 2015-02-03 00:18 ./usr/share/samtools/test/merge/3.merge.expected.err
--rw-r--r-- root/root 46 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_3.fofn
--rw-r--r-- root/root 15673 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_bam_translate.c
--rw-r--r-- root/root 184 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_header.sam
--rw-r--r-- root/root 2482 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_pretty_header.c
--rw-r--r-- root/root 3531 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_rtrans_build.c
--rw-r--r-- root/root 15077 2015-02-03 00:18 ./usr/share/samtools/test/merge/test_trans_tbl_init.c
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/test/mpileup/
--rw-r--r-- root/root 525 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/1read.bam
--rw-r--r-- root/root 5 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/1read.sam
--rw-r--r-- root/root 1886 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/anomalous.sam
--rw-r--r-- root/root 293 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#ID.bam
--rw-r--r-- root/root 377 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#ID2.bam
--rw-r--r-- root/root 265 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#clip.bam
--rw-r--r-- root/root 299 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad1.bam
--rw-r--r-- root/root 349 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad2.bam
--rw-r--r-- root/root 382 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1#pad3.bam
--rw-r--r-- root/root 29 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1.fa
--rw-r--r-- root/root 26 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/c1.fa.fai
--rw-r--r-- root/root 557 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.bam
--rw-r--r-- root/root 416 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.bam.bai
--rw-r--r-- root/root 13183 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.cram
--rw-r--r-- root/root 75 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.cram.crai
--rw-r--r-- root/root 2033 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#5b.sam
--rw-r--r-- root/root 345315 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#large_seq.bam
--rw-r--r-- root/root 233 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap.bam
--rw-r--r-- root/root 896 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap1.bam
--rw-r--r-- root/root 1344 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce#unmap2.bam
--rw-r--r-- root/root 1060702 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce.fa
--rw-r--r-- root/root 230 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/ce.fa.fai
--rw-r--r-- root/root 252022 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/deep.sam
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/test/mpileup/expected/
--rw-r--r-- root/root 1336220 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/1.out.xz
--rw-r--r-- root/root 607 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/10.out
--rw-r--r-- root/root 238 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/11.out
--rw-r--r-- root/root 306 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/12.out
--rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/13.out
--rw-r--r-- root/root 282158 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/14.out
--rw-r--r-- root/root 282158 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/15.out
--rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/16.out
--rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/17.out
--rw-r--r-- root/root 163523 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/18.out
--rw-r--r-- root/root 163385 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/19.out
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--rw-r--r-- root/root 111941 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/45.out
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--rw-r--r-- root/root 384139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/48.out
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--rw-r--r-- root/root 244 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/5.out
--rw-r--r-- root/root 428319 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/50.out
--rw-r--r-- root/root 404654 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/51.out
--rw-r--r-- root/root 37 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/52.out
--rw-r--r-- root/root 138 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/53.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/54.out
--rw-r--r-- root/root 139 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/55.out
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--rw-r--r-- root/root 138 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/58.out
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--rw-r--r-- root/root 362 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/6.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/60.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/61.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/62.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/63.out
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--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/65.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/66.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/67.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/68.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/69.out
--rw-r--r-- root/root 458 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/7.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/70.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/71.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/72.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/73.out
--rw-r--r-- root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/74.out
--rw-r--r-- root/root 140 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/75.out
--rw-r--r-- root/root 221725 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/76.out
--rw-r--r-- root/root 318473 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/77.out
--rw-r--r-- root/root 204 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/8.out
--rw-r--r-- root/root 137 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/expected/9.out
--rw-r--r-- root/root 1561 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/indels.sam
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/
--rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/02099b2aad2cfe707759353724fb40ae
--rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/0d4dfc45807d6a11439e858605cb364d
--rw-r--r-- root/root 4200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/351f64d4f4f9ddd45b35336ad97aa6de
--rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/6ec590eb82c361a61e6baabce20109bc
--rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/6f60cdf4c739651ae72d53e2e94825c1
--rw-r--r-- root/root 200 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/md5/73d180d5cb3860a2713927b6812eab0e
--rw-r--r-- root/root 280 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup-E.bam
--rw-r--r-- root/root 71637 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.1.bam
--rw-r--r-- root/root 776 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.1.bam.bai
--rw-r--r-- root/root 31556 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.2.bam
--rw-r--r-- root/root 31216 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.3.bam
--rw-r--r-- root/root 4284 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.ref.fa
--rw-r--r-- root/root 17 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.ref.fa.fai
--rw-r--r-- root/root 7616 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/mpileup.reg
--rw-r--r-- root/root 793 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/overlap50.sam
--rw-r--r-- root/root 583 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/overlapIllumina.bam
--rw-r--r-- root/root 250 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/regions
--rwxr-xr-x root/root 4687 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/regression.sh
--rw-r--r-- root/root 215 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx#minimal.bam
--rw-r--r-- root/root 247 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx#triplet.bam
--rw-r--r-- root/root 56 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx.fa
--rw-r--r-- root/root 29 2015-02-03 00:18 ./usr/share/samtools/test/mpileup/xx.fa.fai
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/samtools/test/split/
--rw-r--r-- root/root 3597 2015-02-03 00:18 ./usr/share/samtools/test/split/test_count_rg.c
--rw-r--r-- root/root 3951 2015-02-03 00:18 ./usr/share/samtools/test/split/test_expand_format_string.c
--rw-r--r-- root/root 5173 2015-02-03 00:18 ./usr/share/samtools/test/split/test_filter_header_rg.c
--rw-r--r-- root/root 6815 2015-02-03 00:18 ./usr/share/samtools/test/split/test_parse_args.c
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/stat/
--rw-r--r-- root/root 61486 2015-02-03 00:18 ./usr/share/samtools/test/stat/1.stats.expected
--rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/1_map_cigar.sam
--rw-r--r-- root/root 61485 2015-02-03 00:18 ./usr/share/samtools/test/stat/2.stats.expected
--rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/2_equal_cigar_full_seq.sam
--rw-r--r-- root/root 60454 2015-02-03 00:18 ./usr/share/samtools/test/stat/3.stats.expected
--rw-r--r-- root/root 232 2015-02-03 00:18 ./usr/share/samtools/test/stat/3_map_cigar_equal_seq.sam
--rw-r--r-- root/root 61486 2015-02-03 00:18 ./usr/share/samtools/test/stat/4.stats.expected
--rw-r--r-- root/root 234 2015-02-03 00:18 ./usr/share/samtools/test/stat/4_X_cigar_full_seq.sam
--rw-r--r-- root/root 61508 2015-02-03 00:18 ./usr/share/samtools/test/stat/5.stats.expected
--rw-r--r-- root/root 236 2015-02-03 00:18 ./usr/share/samtools/test/stat/5_insert_cigar.sam
--rw-r--r-- root/root 61508 2015-02-03 00:18 ./usr/share/samtools/test/stat/6.stats.expected
--rw-r--r-- root/root 109 2015-02-03 00:18 ./usr/share/samtools/test/stat/test.fa
--rw-r--r-- root/root 18 2015-02-03 00:18 ./usr/share/samtools/test/stat/test.fa.fai
--rw-r--r-- root/root 1990 2015-02-03 00:18 ./usr/share/samtools/test/test.c
--rw-r--r-- root/root 1361 2015-02-03 00:18 ./usr/share/samtools/test/test.h
--rwxr-xr-x root/root 83362 2015-02-03 00:18 ./usr/share/samtools/test/test.pl
-drwxr-xr-x root/root 0 2015-02-03 00:18 ./usr/share/samtools/test/tview/
--rw-r--r-- root/root 2424 2015-02-03 00:18 ./usr/share/samtools/test/tview/test_get_rg_sample.c
--rw-r--r-- root/root 3455 2015-02-03 00:18 ./usr/share/samtools/test/vcf-miniview.c
-
-
-samtools_1.2-2_amd64.deb
-────────────────────────
-
- new debian package, version 2.0.
- size 75450 bytes: control archive=1426 bytes.
- 764 bytes, 16 lines control
- 1467 bytes, 26 lines md5sums
- Package: samtools
- Version: 1.2-2
- Architecture: amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 291
- Depends: libc6 (>= 2.14), libhts1 (>= 1.0), 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
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/bin/
--rwxr-xr-x root/root 22664 2015-09-17 20:25 ./usr/bin/ace2sam
--rwxr-xr-x root/root 5328 2015-02-03 00:18 ./usr/bin/blast2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/blast2sam.pl -> blast2sam
--rwxr-xr-x root/root 3364 2015-02-03 00:18 ./usr/bin/bowtie2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/bowtie2sam.pl -> bowtie2sam
--rwxr-xr-x root/root 18032 2015-02-03 00:18 ./usr/bin/export2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/export2sam.pl -> export2sam
--rwxr-xr-x root/root 6125 2015-02-03 00:18 ./usr/bin/interpolate_sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/interpolate_sam.pl -> interpolate_sam
--rwxr-xr-x root/root 10336 2015-09-17 20:25 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10336 2015-09-17 20:25 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14440 2015-09-17 20:25 ./usr/bin/md5fa
--rwxr-xr-x root/root 10280 2015-09-17 20:25 ./usr/bin/md5sum-lite
--rwxr-xr-x root/root 6773 2015-02-03 00:18 ./usr/bin/novo2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/novo2sam.pl -> novo2sam
--rwxr-xr-x root/root 48036 2015-02-03 00:18 ./usr/bin/plot-bamstats
--rwxr-xr-x root/root 3208 2015-02-03 00:18 ./usr/bin/psl2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/psl2sam.pl -> psl2sam
--rwxr-xr-x root/root 8961 2015-02-03 00:18 ./usr/bin/sam2vcf
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/sam2vcf.pl -> sam2vcf
--rwxr-xr-x root/root 16478 2015-02-03 00:18 ./usr/bin/samtools
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/samtools.pl -> samtools
--rwxr-xr-x root/root 11105 2015-02-03 00:18 ./usr/bin/seq_cache_populate
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/seq_cache_populate.pl -> seq_cache_populate
--rwxr-xr-x root/root 3909 2015-02-03 00:18 ./usr/bin/soap2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/soap2sam.pl -> soap2sam
--rwxr-xr-x root/root 7888 2015-02-03 00:18 ./usr/bin/varfilter
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/varfilter.py -> varfilter
--rwxr-xr-x root/root 22752 2015-09-17 20:25 ./usr/bin/wgsim
--rwxr-xr-x root/root 4157 2015-02-03 00:18 ./usr/bin/wgsim_eval
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/wgsim_eval.pl -> wgsim_eval
--rwxr-xr-x root/root 3583 2015-02-03 00:18 ./usr/bin/zoom2sam
-lrwxrwxrwx root/root 0 2015-09-17 20:25 ./usr/bin/zoom2sam.pl -> zoom2sam
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/doc/samtools/
--rw-r--r-- root/root 828 2015-02-03 00:18 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1031 2015-09-17 20:15 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3542 2015-09-17 20:22 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 3462 2015-09-17 20:15 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 592 2015-09-17 20:15 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/man/
-drwxr-xr-x root/root 0 2015-09-17 20:25 ./usr/share/man/man1/
--rw-r--r-- root/root 12907 2015-09-17 20:25 ./usr/share/man/man1/samtools.1.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Cleanup │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /«BUILDDIR»
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bash-completion* bsdmainutils* debhelper* file* gettext* gettext-base*
- groff-base* intltool-debian* libcroco3* libffi6* libglib2.0-0* libhts-dev*
- libhts1* libicu55* libio-pty-perl* libmagic1* libncurses5-dev* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf*
- sbuild-build-depends-core-dummy* sbuild-build-depends-samtools-dummy* tabix*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 27 to remove and 0 not upgraded.
-After this operation, 65.3 MB disk space will be freed.
-(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 14078 files and directories currently installed.)
-Removing sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Removing bash-completion (1:2.1-4.2) ...
-Purging configuration files for bash-completion (1:2.1-4.2) ...
-Removing debhelper (9.20150811) ...
-Removing man-db (2.7.3-1) ...
-Purging configuration files for man-db (2.7.3-1) ...
-Removing bsdmainutils (9.0.6) ...
-Purging configuration files for bsdmainutils (9.0.6) ...
-Removing file (1:5.24-2) ...
-Removing po-debconf (1.0.18) ...
-Removing intltool-debian (0.35.0+20060710.4) ...
-Removing gettext (0.19.6-1) ...
-Removing gettext-base (0.19.6-1) ...
-Removing groff-base (1.22.3-1) ...
-Purging configuration files for groff-base (1.22.3-1) ...
-Removing libcroco3:amd64 (0.6.8-3+b1) ...
-Purging configuration files for libcroco3:amd64 (0.6.8-3+b1) ...
-Removing libglib2.0-0:amd64 (2.44.1-1.1) ...
-Purging configuration files for libglib2.0-0:amd64 (2.44.1-1.1) ...
-Removing libffi6:amd64 (3.2.1-3) ...
-Purging configuration files for libffi6:amd64 (3.2.1-3) ...
-Removing libhts-dev:amd64 (1.2.1-1) ...
-Removing libhts1:amd64 (1.2.1-1) ...
-Purging configuration files for libhts1:amd64 (1.2.1-1) ...
-Removing libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
-Purging configuration files for libxml2:amd64 (2.9.2+really2.9.1+dfsg1-0.2) ...
-Removing libicu55:amd64 (55.1-5) ...
-Purging configuration files for libicu55:amd64 (55.1-5) ...
-Removing libio-pty-perl (1:1.08-1+b4) ...
-Removing libmagic1:amd64 (1:5.24-2) ...
-Purging configuration files for libmagic1:amd64 (1:5.24-2) ...
-Removing libncurses5-dev:amd64 (6.0+20150810-1) ...
-Removing libpipeline1:amd64 (1.4.1-1) ...
-Purging configuration files for libpipeline1:amd64 (1.4.1-1) ...
-Removing libtinfo-dev:amd64 (6.0+20150810-1) ...
-Removing libunistring0:amd64 (0.9.3-5.2+b1) ...
-Purging configuration files for libunistring0:amd64 (0.9.3-5.2+b1) ...
-Removing sbuild-build-depends-core-dummy (0.invalid.0) ...
-Removing tabix (1.2.1-1) ...
-Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
-Processing triggers for libc-bin (2.19-20) ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build Architecture: amd64
-Build-Space: 24836
-Build-Time: 66
-Distribution: unstable
-Host Architecture: amd64
-Install-Time: 20
-Job: samtools_1.2-2.dsc
-Machine Architecture: amd64
-Package: samtools
-Package-Time: 89
-Source-Version: 1.2-2
-Space: 24836
-Status: successful
-Version: 1.2-2
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20150917-2025
-Build needed 00:01:29, 24836k disc space
diff --git a/arm64.log b/arm64.log
index 2a47d85..e0e0b3f 100644
--- a/arm64.log
+++ b/arm64.log
@@ -1,76 +1,45 @@
-From buildd at arm-arm-02.debian.org Thu Sep 25 05:29:23 2014
-Return-path: <buildd at arm-arm-02.debian.org>
-Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at arm-arm-02.debian.org>)
- id 1XX1cI-0004X5-PQ
- for logs at buildd.debian.org; Thu, 25 Sep 2014 05:29:22 +0000
-Received: from alwyn.islands.arm.com ([217.140.96.59]
- helo=arm-arm-02.debian.org)
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=arm-arm-02.debian.org, EMAIL=hostmaster at arm-arm-02.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at arm-arm-02.debian.org>)
- id 1XX1cF-0005Go-4K
- for logs at buildd.debian.org; Thu, 25 Sep 2014 05:29:20 +0000
-Received: from buildd by arm-arm-02.debian.org with local (Exim 4.80)
- (envelope-from <buildd at arm-arm-02.debian.org>)
- id 1XX1cA-0004Rk-Hr; Thu, 25 Sep 2014 05:29:14 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 05:29:14 +0000
-From: buildd on arm-arm-02 <buildd at arm-arm-02.debian.org>
-To: buildd-porters at arm-arm-02.debian.org,
- logs at buildd.debian.org
-Subject: Log for attempted build of samtools_1.1-1 on arm64 (dist=sid)
-Key-Id: 9EA3BEB5
-Message-Id: <E1XX1cA-0004Rk-Hr at arm-arm-02.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on arm-arm-02.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on arm-arm-03.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (arm64) 25 Sep 2014 00:25 ║
+║ samtools 1.2-3 (arm64) 22 Sep 2015 16:03 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
-Machine Architecture: armhf
+Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
-I: NOTICE: Log filtering will replace 'build/samtools-AekwtD/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-AekwtD' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-871154a1-ba07-424d-b1df-148f48b013a7' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-y9iLsV/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-y9iLsV' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-arm64-sbuild-516aafa4-0414-4d26-87f4-6f04e0618260' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org unstable InRelease [233 kB]
-Get:2 http://ftp.uk.debian.org unstable InRelease [233 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:4 http://ftp.debian.org unstable/main Sources [7548 kB]
-Get:5 http://ftp.uk.debian.org unstable/main Sources [7548 kB]
-Get:6 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
-Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
-Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
-Get:9 http://incoming.debian.org buildd-unstable/main arm64 Packages [332 kB]
-Get:10 http://incoming.debian.org buildd-unstable/contrib arm64 Packages [844 B]
-Get:11 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
-Get:12 http://ftp.debian.org unstable/non-free Sources [107 kB]
-Get:13 http://ftp.debian.org unstable/main arm64 Packages [5808 kB]
-Get:14 http://ftp.debian.org unstable/contrib arm64 Packages [28.4 kB]
-Get:15 http://ftp.uk.debian.org unstable/contrib Sources [57.1 kB]
-Get:16 http://ftp.uk.debian.org unstable/non-free Sources [107 kB]
-Get:17 http://ftp.uk.debian.org unstable/main arm64 Packages [5808 kB]
-Get:18 http://ftp.uk.debian.org unstable/contrib arm64 Packages [28.4 kB]
-Fetched 28.4 MB in 39s (711 kB/s)
+Get:1 http://mirror.bytemark.co.uk unstable InRelease [253 kB]
+Get:2 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:3 http://ftp.debian.org unstable InRelease [253 kB]
+Get:4 http://incoming.debian.org buildd-unstable/main Sources [341 kB]
+Get:5 http://mirror.bytemark.co.uk unstable/main Sources [8093 kB]
+Get:6 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:7 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
+Get:8 http://incoming.debian.org buildd-unstable/main arm64 Packages [96.8 kB]
+Get:9 http://incoming.debian.org buildd-unstable/contrib arm64 Packages [1052 B]
+Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:11 http://mirror.bytemark.co.uk unstable/contrib Sources [59.7 kB]
+Get:12 http://mirror.bytemark.co.uk unstable/non-free Sources [106 kB]
+Get:13 http://mirror.bytemark.co.uk unstable/main arm64 Packages [7240 kB]
+Get:14 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:15 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:16 http://ftp.debian.org unstable/main arm64 Packages [7240 kB]
+Get:17 http://mirror.bytemark.co.uk unstable/contrib arm64 Packages [43.2 kB]
+Get:18 http://ftp.debian.org unstable/contrib arm64 Packages [43.2 kB]
+Fetched 32.1 MB in 9s (3342 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -91,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 2s (1724 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 0s (16.0 MB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-0BR0BW/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-8B3d39/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -118,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
-Need to get 0 B/820 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/772 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11543 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-aJizjS/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11753 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-Az_CnA/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -142,165 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf tabix zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-0 upgraded, 25 newly installed, 0 to remove and 3 not upgraded.
-Need to get 9547 kB/9548 kB of archives.
-After this operation, 29.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 arm64 1.3.1-1 [23.6 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base arm64 1.22.2-8 [1141 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils arm64 9.0.5+b3 [178 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db arm64 2.7.0.1-1 [973 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 arm64 0.19.2-2+b1 [30.9 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 arm64 1:5.19-2 [231 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libxml2 arm64 2.9.1+dfsg1-4+b2 [692 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libffi6 arm64 3.1-2+b2 [18.9 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 arm64 2.42.0-1 [2295 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 arm64 0.6.8-3 [119 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libhts1 arm64 1.1-1 [171 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main file arm64 1:5.19-2 [58.2 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext-base arm64 0.19.2-2+b1 [118 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext arm64 0.19.2-2+b1 [1175 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev arm64 1.1-1 [225 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev arm64 5.9+20140913-1+b1 [71.7 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev arm64 5.9+20140913-1+b1 [163 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main tabix arm64 1.1-1 [160 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev arm64 1:1.2.8.dfsg-2 [200 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 17.5 MB/17.5 MB of archives.
+After this operation, 63.8 MB of additional disk space will be used.
+Get:1 http://mirror.bytemark.co.uk/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://mirror.bytemark.co.uk/debian/ unstable/main groff-base arm64 1.22.3-1 [1166 kB]
+Get:3 http://mirror.bytemark.co.uk/debian/ unstable/main bsdmainutils arm64 9.0.6 [179 kB]
+Get:4 http://mirror.bytemark.co.uk/debian/ unstable/main libpipeline1 arm64 1.4.1-1 [24.8 kB]
+Get:5 http://mirror.bytemark.co.uk/debian/ unstable/main man-db arm64 2.7.3-1 [975 kB]
+Get:6 http://mirror.bytemark.co.uk/debian/ unstable/main libffi6 arm64 3.2.1-3 [18.7 kB]
+Get:7 http://mirror.bytemark.co.uk/debian/ unstable/main libglib2.0-0 arm64 2.44.1-1.1 [2266 kB]
+Get:8 http://mirror.bytemark.co.uk/debian/ unstable/main libicu55 arm64 55.1-5 [7487 kB]
+Get:9 http://mirror.bytemark.co.uk/debian/ unstable/main libxml2 arm64 2.9.2+zdfsg1-4 [781 kB]
+Get:10 http://mirror.bytemark.co.uk/debian/ unstable/main libcroco3 arm64 0.6.8-3+b1 [120 kB]
+Get:11 http://mirror.bytemark.co.uk/debian/ unstable/main libunistring0 arm64 0.9.3-5.2+b2 [257 kB]
+Get:12 http://mirror.bytemark.co.uk/debian/ unstable/main libmagic1 arm64 1:5.25-1 [248 kB]
+Get:13 http://mirror.bytemark.co.uk/debian/ unstable/main file arm64 1:5.25-1 [61.5 kB]
+Get:14 http://mirror.bytemark.co.uk/debian/ unstable/main gettext-base arm64 0.19.6-1 [120 kB]
+Get:15 http://mirror.bytemark.co.uk/debian/ unstable/main gettext arm64 0.19.6-1 [1406 kB]
+Get:16 http://mirror.bytemark.co.uk/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://mirror.bytemark.co.uk/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://mirror.bytemark.co.uk/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://mirror.bytemark.co.uk/debian/ unstable/main libhts1 arm64 1.2.1-1 [191 kB]
+Get:20 http://mirror.bytemark.co.uk/debian/ unstable/main libhts-dev arm64 1.2.1-1 [249 kB]
+Get:21 http://mirror.bytemark.co.uk/debian/ unstable/main libio-pty-perl arm64 1:1.08-1+b1 [34.5 kB]
+Get:22 http://mirror.bytemark.co.uk/debian/ unstable/main libtinfo-dev arm64 6.0+20150810-1 [71.4 kB]
+Get:23 http://mirror.bytemark.co.uk/debian/ unstable/main libncurses5-dev arm64 6.0+20150810-1 [160 kB]
+Get:24 http://mirror.bytemark.co.uk/debian/ unstable/main tabix arm64 1.2.1-1 [186 kB]
+Get:25 http://mirror.bytemark.co.uk/debian/ unstable/main zlib1g-dev arm64 1:1.2.8.dfsg-2+b1 [200 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9547 kB in 44s (216 kB/s)
-Selecting previously unselected package libpipeline1:arm64.
-(Reading database ... 11543 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_arm64.deb ...
-Unpacking libpipeline1:arm64 (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_arm64.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5+b3_arm64.deb ...
-Unpacking bsdmainutils (9.0.5+b3) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_arm64.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:arm64.
-Preparing to unpack .../libasprintf0c2_0.19.2-2+b1_arm64.deb ...
-Unpacking libasprintf0c2:arm64 (0.19.2-2+b1) ...
-Selecting previously unselected package libmagic1:arm64.
-Preparing to unpack .../libmagic1_1%3a5.19-2_arm64.deb ...
-Unpacking libmagic1:arm64 (1:5.19-2) ...
-Selecting previously unselected package libxml2:arm64.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4+b2_arm64.deb ...
-Unpacking libxml2:arm64 (2.9.1+dfsg1-4+b2) ...
-Selecting previously unselected package libffi6:arm64.
-Preparing to unpack .../libffi6_3.1-2+b2_arm64.deb ...
-Unpacking libffi6:arm64 (3.1-2+b2) ...
-Selecting previously unselected package libglib2.0-0:arm64.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_arm64.deb ...
-Unpacking libglib2.0-0:arm64 (2.42.0-1) ...
-Selecting previously unselected package libcroco3:arm64.
-Preparing to unpack .../libcroco3_0.6.8-3_arm64.deb ...
-Unpacking libcroco3:arm64 (0.6.8-3) ...
-Selecting previously unselected package libhts1:arm64.
-Preparing to unpack .../libhts1_1.1-1_arm64.deb ...
-Unpacking libhts1:arm64 (1.1-1) ...
-Selecting previously unselected package libunistring0:arm64.
-Preparing to unpack .../libunistring0_0.9.3-5.2+b2_arm64.deb ...
-Unpacking libunistring0:arm64 (0.9.3-5.2+b2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_arm64.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2+b1_arm64.deb ...
-Unpacking gettext-base (0.19.2-2+b1) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2+b1_arm64.deb ...
-Unpacking gettext (0.19.2-2+b1) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:arm64.
-Preparing to unpack .../libhts-dev_1.1-1_arm64.deb ...
-Unpacking libhts-dev:arm64 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:arm64.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1+b1_arm64.deb ...
-Unpacking libtinfo-dev:arm64 (5.9+20140913-1+b1) ...
-Selecting previously unselected package libncurses5-dev:arm64.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1+b1_arm64.deb ...
-Unpacking libncurses5-dev:arm64 (5.9+20140913-1+b1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.1-1_arm64.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:arm64.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_arm64.deb ...
-Unpacking zlib1g-dev:arm64 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:arm64 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5+b3) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:arm64 (0.19.2-2+b1) ...
-Setting up libmagic1:arm64 (1:5.19-2) ...
-Setting up libxml2:arm64 (2.9.1+dfsg1-4+b2) ...
-Setting up libffi6:arm64 (3.1-2+b2) ...
-Setting up libglib2.0-0:arm64 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:arm64 (0.6.8-3) ...
-Setting up libhts1:arm64 (1.1-1) ...
-Setting up libunistring0:arm64 (0.9.3-5.2+b2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2+b1) ...
-Setting up gettext (0.19.2-2+b1) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:arm64 (1.1-1) ...
-Setting up libtinfo-dev:arm64 (5.9+20140913-1+b1) ...
-Setting up libncurses5-dev:arm64 (5.9+20140913-1+b1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Fetched 17.5 MB in 1s (14.6 MB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 11753 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_arm64.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_arm64.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:arm64.
+Preparing to unpack .../libpipeline1_1.4.1-1_arm64.deb ...
+Unpacking libpipeline1:arm64 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_arm64.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:arm64.
+Preparing to unpack .../libffi6_3.2.1-3_arm64.deb ...
+Unpacking libffi6:arm64 (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:arm64.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_arm64.deb ...
+Unpacking libglib2.0-0:arm64 (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:arm64.
+Preparing to unpack .../libicu55_55.1-5_arm64.deb ...
+Unpacking libicu55:arm64 (55.1-5) ...
+Selecting previously unselected package libxml2:arm64.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_arm64.deb ...
+Unpacking libxml2:arm64 (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:arm64.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_arm64.deb ...
+Unpacking libcroco3:arm64 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:arm64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b2_arm64.deb ...
+Unpacking libunistring0:arm64 (0.9.3-5.2+b2) ...
+Selecting previously unselected package libmagic1:arm64.
+Preparing to unpack .../libmagic1_1%3a5.25-1_arm64.deb ...
+Unpacking libmagic1:arm64 (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_arm64.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_arm64.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_arm64.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:arm64.
+Preparing to unpack .../libhts1_1.2.1-1_arm64.deb ...
+Unpacking libhts1:arm64 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:arm64.
+Preparing to unpack .../libhts-dev_1.2.1-1_arm64.deb ...
+Unpacking libhts-dev:arm64 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b1_arm64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b1) ...
+Selecting previously unselected package libtinfo-dev:arm64.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_arm64.deb ...
+Unpacking libtinfo-dev:arm64 (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:arm64.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_arm64.deb ...
+Unpacking libncurses5-dev:arm64 (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_arm64.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:arm64 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:arm64 (3.2.1-3) ...
+Setting up libglib2.0-0:arm64 (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:arm64 (55.1-5) ...
+Setting up libxml2:arm64 (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:arm64 (0.6.8-3+b1) ...
+Setting up libunistring0:arm64 (0.9.3-5.2+b2) ...
+Setting up libmagic1:arm64 (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:arm64 (1.2.1-1) ...
+Setting up libhts-dev:arm64 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b1) ...
+Setting up libtinfo-dev:arm64 (6.0+20150810-1) ...
+Setting up libncurses5-dev:arm64 (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:arm64 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16.0 armhf (aarch64)
-Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-2
-Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.1 base-files_7.5+b2 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5+b3 bsdutils_1:2.20.1-5.8+b2 build-essential_11.7 bzip2_1.0.6-7+b2 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4+b2 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4+b2 diffutils_1:3.3-1+b2 dmsetup_2:1.02.90-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_ [...]
+Kernel: Linux 3.16.0-4-arm64 arm64 (aarch64)
+Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b3 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b3 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -311,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -339,7 +326,7 @@ SCHROOT_CHROOT_NAME=sid-arm64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-arm64-sbuild-871154a1-ba07-424d-b1df-148f48b013a7
+SCHROOT_SESSION_ID=sid-arm64-sbuild-516aafa4-0414-4d26-87f4-6f04e0618260
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -349,11 +336,11 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture arm64
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -373,9 +360,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -412,8 +401,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -458,6 +446,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
@@ -467,13 +456,13 @@ gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lcurs [...]
gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lcurses -lm -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/aarch64-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -485,39 +474,1229 @@ dh_auto_test -- \
make -j6 test HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/PMW4HD3gTH/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/9A0dTCZs8w/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/9A0dTCZs8w/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/9A0dTCZs8w/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/9A0dTCZs8w/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/9A0dTCZs8w/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/9A0dTCZs8w/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/9A0dTCZs8w/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/9A0dTCZs8w/mpileup.bam.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9A0dTCZs8w/mpileup.bam.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/9A0dTCZs8w/mpileup.cram.list -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9A0dTCZs8w/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/9A0dTCZs8w/mpileup.ref.fa.gz -r17:1050-1060 /tmp/9A0dTCZs8w/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/PMW4HD3gTH/bgzip.dat.gz
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/PMW4HD3gTH/bgzip.dat.gz
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
.. ok
-Signal caught, cleaning and exiting...
-make[1]: *** [override_dh_auto_test] Terminated
-make[2]: *** wait: No child processes. Stop.
-make[2]: *** Waiting for unfinished jobs....
-make[2]: *** wait: No child processes. Stop.
-E: Caught signal ‘Terminated’: terminating immediately
-make: *** [build-arch] Terminated
-debian/rules:18: recipe for target 'override_dh_auto_test' failed
-debian/rules:6: recipe for target 'build-arch' failed
-The command failed [15]: /«PKGBUILDDIR»/samtools faidx /tmp/PMW4HD3gTH/faidx.fa
-out:
-err:
- at test/test.pl line 67.
- main::error("The command failed [15]: /«PKGBUILDDIR»/"..., "out:\x{a}", "err:\x{a}") called at test/test.pl line 138
- main::cmd("/«PKGBUILDDIR»/samtools faidx /tmp/PMW4H"...) called at test/test.pl line 390
- main::test_faidx(HASH(0x13b5fec8)) called at test/test.pl line 36
-Build killed with signal TERM after 300 minutes of inactivity
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 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/9A0dTCZs8w/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/9A0dTCZs8w/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/9A0dTCZs8w/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/9A0dTCZs8w/view.test067.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/9A0dTCZs8w/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/9A0dTCZs8w/view.test069.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/9A0dTCZs8w/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/9A0dTCZs8w/view.test071.sam -h -l Library 2 /tmp/9A0dTCZs8w/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/9A0dTCZs8w/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input) .. ok
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input) .. ok
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input) .. ok
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input) .. ok
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input) .. ok
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input) .. ok
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input) .. ok
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input) .. ok
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input) .. ok
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input) .. ok
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input) .. ok
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input) .. ok
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input) .. ok
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input) .. ok
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input) .. ok
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: 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
+
+ 194: 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
+
+ 196: 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
+
+ 198: 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
+
+ 200: 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
+
+ 202: 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
+
+ 204: 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
+
+ 206: 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
+
+ 208: 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
+
+ 210: 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
+
+ 212: 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
+
+ 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:30 (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:10-30 (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:10-30 (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:25-35 (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:25-35 (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.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
+
+ 227: 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
+
+ 229: 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
+
+ 231: 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
+
+ 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 -r grp1 (CRAM 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 -f 128 (BAM 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 -f 128 (CRAM 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 -q 5 (BAM 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 -q 5 (CRAM 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 -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
+
+ 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 -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags .. ok
+
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 261: Make CRAM with no UR field .. ok
+
+ 262: Decoding CRAM with no UR field via -T .. ok
+
+ 263: CIGAR B-operator removal .. ok
+
+ 264: Big SAM -> BAM .. ok
+
+ 265: Big SAM -> BAM (2 threads) .. ok
+
+ 266: Big SAM -> BAM (4 threads) .. ok
+
+ 267: Big SAM -> CRAM .. ok
+
+ 268: Big SAM -> CRAM (2 threads) .. ok
+
+ 269: Big SAM -> CRAM (4 threads) .. ok
+
+ 270: Subsample 0.2 (SAM input) ............ ok
+
+ 271: Subsample 0.5 (SAM input) ............ ok
+
+ 272: Subsample 0.8 (SAM input) ............ ok
+
+ 273: Subsample 0.2 (BAM input) ............ ok
+
+ 274: Subsample 0.5 (BAM input) ............ ok
+
+ 275: Subsample 0.8 (BAM input) ............ ok
+
+ 276: Subsample 0.2 (CRAM input) ............ ok
+
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file .. ok
+
+Unsorted mode enabled
+ Generate CRAM file .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/9A0dTCZs8w/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/9A0dTCZs8w/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/9A0dTCZs8w/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/9A0dTCZs8w/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. 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/pBv3PCkKtv - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. 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
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a
+ install -d debian/samtools
+ make -j6 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/aarch64-linux-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/aarch64-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_arm64.deb'.
+ dpkg-genchanges -B -marm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org> >../samtools_1.2-3_arm64.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0529
+Build finished at 20150922-1615
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_arm64.changes:
+─────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: arm64
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: arm Build Daemon (arm-arm-03) <buildd_arm64-arm-arm-03 at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ f0055fe5ae88f389a16280028ab27c84af91e2c5 347256 samtools_1.2-3_arm64.deb
+Checksums-Sha256:
+ 82a56ba46b0a2f5dd2bb75dd2d068d2266e9293ac1a76ac60108a90ddd4abbfb 347256 samtools_1.2-3_arm64.deb
+Files:
+ 8eb0693afe625864b624591d015d3573 347256 science optional samtools_1.2-3_arm64.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_arm64.deb
+────────────────────────
+
+ new debian package, version 2.0.
+ size 347256 bytes: control archive=1484 bytes.
+ 802 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: arm64
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 957
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/bin/
+-rwxr-xr-x root/root 18480 2015-09-22 16:15 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10256 2015-09-22 16:15 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10256 2015-09-22 16:15 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14352 2015-09-22 16:15 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10200 2015-09-22 16:15 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 695776 2015-09-22 16:15 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 26760 2015-09-22 16:15 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 16:15 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 16:15 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -531,20 +1710,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: arm64
-Build-Space: 23848
-Build-Time: 18043
+Build-Space: 15120
+Build-Time: 718
Distribution: sid
-Fail-Stage: build
Host Architecture: arm64
-Install-Time: 93
-Job: samtools_1.1-1
-Machine Architecture: armhf
+Install-Time: 13
+Job: samtools_1.2-3
+Machine Architecture: arm64
Package: samtools
-Package-Time: 18199
-Source-Version: 1.1-1
-Space: 23848
-Status: attempted
-Version: 1.1-1
+Package-Time: 755
+Source-Version: 1.2-3
+Space: 15120
+Status: successful
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0529
-Build needed 05:03:19, 23848k disc space
+Finished at 20150922-1615
+Build needed 00:12:35, 15120k disc space
+Signature with key 'FD6F04EA' requested:
+ signfile /home/buildd/build/samtools_1.2-3_arm64.changes FD6F04EA
+
+Successfully signed changes file
diff --git a/armel.log b/armel.log
index e69de29..14c408a 100644
--- a/armel.log
+++ b/armel.log
@@ -0,0 +1,1732 @@
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on antheil.debian.org
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.2-3 (armel) 22 Sep 2015 16:17 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.2-3
+Source Version: 1.2-3
+Distribution: sid
+Machine Architecture: armel
+Host Architecture: armel
+Build Architecture: armel
+
+I: NOTICE: Log filtering will replace 'build/samtools-gPwsTX/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-gPwsTX' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-armel-sbuild-f32f02fb-b239-4cfc-bdbc-eb43798d193b' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.uk.debian.org unstable InRelease [253 kB]
+Get:2 http://ftp.debian.org unstable InRelease [253 kB]
+Get:3 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:5 http://ftp.uk.debian.org unstable/main Sources [8093 kB]
+Get:6 http://incoming.debian.org buildd-unstable/main Sources [354 kB]
+Get:7 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:8 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:9 http://ftp.debian.org unstable/main armel Packages [7409 kB]
+Get:10 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:11 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
+Get:12 http://ftp.debian.org unstable/contrib armel Packages [45.2 kB]
+Get:13 http://incoming.debian.org buildd-unstable/main armel Packages [101 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib armel Packages [1056 B]
+Get:15 http://ftp.uk.debian.org unstable/contrib Sources [59.7 kB]
+Get:16 http://ftp.uk.debian.org unstable/non-free Sources [106 kB]
+Get:17 http://ftp.uk.debian.org unstable/main armel Packages [7409 kB]
+Get:18 http://ftp.uk.debian.org unstable/contrib armel Packages [45.2 kB]
+Fetched 32.5 MB in 32s (988 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 8s (533 kB/s)
+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-2tF7AU/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following NEW packages will be installed:
+ sbuild-build-depends-core-dummy
+debconf: delaying package configuration, since apt-utils is not installed
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/774 B of archives.
+After this operation, 0 B of additional disk space will be used.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 11623 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-uP4prh/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
+Suggested packages:
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
+Recommended packages:
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 17.3 MB/17.3 MB of archives.
+After this operation, 64.3 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armel 1.22.3-1 [1123 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armel 9.0.6 [178 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armel 1.4.1-1 [23.5 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db armel 2.7.3-1 [977 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi6 armel 3.2.1-3 [18.3 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armel 2.44.1-1.1 [2312 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libicu55 armel 55.1-5 [7341 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armel 2.9.2+zdfsg1-4 [801 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armel 0.6.8-3+b1 [124 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armel 0.9.3-5.2+b1 [253 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armel 1:5.25-1 [251 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main file armel 1:5.25-1 [61.1 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armel 0.19.6-1 [119 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext armel 0.19.6-1 [1399 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libhts1 armel 1.2.1-1 [193 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev armel 1.2.1-1 [241 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main libio-pty-perl armel 1:1.08-1+b4 [35.2 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armel 6.0+20150810-1 [66.4 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armel 6.0+20150810-1 [155 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main tabix armel 1.2.1-1 [183 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armel 1:1.2.8.dfsg-2+b1 [200 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 17.3 MB in 7s (2209 kB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 11623 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_armel.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_armel.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:armel.
+Preparing to unpack .../libpipeline1_1.4.1-1_armel.deb ...
+Unpacking libpipeline1:armel (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_armel.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:armel.
+Preparing to unpack .../libffi6_3.2.1-3_armel.deb ...
+Unpacking libffi6:armel (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:armel.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_armel.deb ...
+Unpacking libglib2.0-0:armel (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:armel.
+Preparing to unpack .../libicu55_55.1-5_armel.deb ...
+Unpacking libicu55:armel (55.1-5) ...
+Selecting previously unselected package libxml2:armel.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_armel.deb ...
+Unpacking libxml2:armel (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:armel.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_armel.deb ...
+Unpacking libcroco3:armel (0.6.8-3+b1) ...
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+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_armel.deb ...
+Unpacking libunistring0:armel (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:armel.
+Preparing to unpack .../libmagic1_1%3a5.25-1_armel.deb ...
+Unpacking libmagic1:armel (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_armel.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_armel.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_armel.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:armel.
+Preparing to unpack .../libhts1_1.2.1-1_armel.deb ...
+Unpacking libhts1:armel (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:armel.
+Preparing to unpack .../libhts-dev_1.2.1-1_armel.deb ...
+Unpacking libhts-dev:armel (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_armel.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:armel.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_armel.deb ...
+Unpacking libtinfo-dev:armel (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:armel.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_armel.deb ...
+Unpacking libncurses5-dev:armel (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_armel.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:armel (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:armel (3.2.1-3) ...
+Setting up libglib2.0-0:armel (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:armel (55.1-5) ...
+Setting up libxml2:armel (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:armel (0.6.8-3+b1) ...
+Setting up libunistring0:armel (0.9.3-5.2+b1) ...
+Setting up libmagic1:armel (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:armel (1.2.1-1) ...
+Setting up libhts-dev:armel (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:armel (6.0+20150810-1) ...
+Setting up libncurses5-dev:armel (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:armel (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.16.0-4-armmp-lpae armel (armv7l)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying i386-build.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-armel-sbuild
+SCHROOT_CHROOT_NAME=sid-armel-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=1009
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-armel-sbuild-f32f02fb-b239-4cfc-bdbc-eb43798d193b
+SCHROOT_UID=2952
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.2
+dpkg-buildpackage: host architecture armel
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j4 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -rf debian/.debhelper/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lcurses -lm -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/arm-linux-gnueabi/libhts.a -lhts -lz
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a \
+ BGZIP=/usr/bin/bgzip
+ make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a BGZIP=/usr/bin/bgzip
+make[2]: Entering directory '/«PKGBUILDDIR»'
+REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/pUOoPqG2pH/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/pUOoPqG2pH/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/pUOoPqG2pH/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/pUOoPqG2pH/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/pUOoPqG2pH/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/pUOoPqG2pH/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/pUOoPqG2pH/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/pUOoPqG2pH/mpileup.bam.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pUOoPqG2pH/mpileup.bam.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/pUOoPqG2pH/mpileup.cram.list -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pUOoPqG2pH/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pUOoPqG2pH/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pUOoPqG2pH/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 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/pUOoPqG2pH/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/pUOoPqG2pH/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/pUOoPqG2pH/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pUOoPqG2pH/view.test067.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pUOoPqG2pH/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pUOoPqG2pH/view.test069.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pUOoPqG2pH/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/pUOoPqG2pH/view.test071.sam -h -l Library 2 /tmp/pUOoPqG2pH/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pUOoPqG2pH/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input) .. ok
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input) .. ok
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input) .. ok
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input) .. ok
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input) .. ok
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input) .. ok
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input) .. ok
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input) .. ok
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input) .. ok
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input) .. ok
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input) .. ok
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input) .. ok
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input) .. ok
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input) .. ok
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input) .. ok
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: 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
+
+ 194: 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
+
+ 196: 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
+
+ 198: 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
+
+ 200: 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
+
+ 202: 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
+
+ 204: 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
+
+ 206: 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
+
+ 208: 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
+
+ 210: 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
+
+ 212: 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
+
+ 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:30 (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:10-30 (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:10-30 (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:25-35 (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:25-35 (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.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
+
+ 227: 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
+
+ 229: 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
+
+ 231: 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
+
+ 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 -r grp1 (CRAM 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 -f 128 (BAM 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 -f 128 (CRAM 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 -q 5 (BAM 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 -q 5 (CRAM 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 -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
+
+ 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 -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags .. ok
+
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 261: Make CRAM with no UR field .. ok
+
+ 262: Decoding CRAM with no UR field via -T .. ok
+
+ 263: CIGAR B-operator removal .. ok
+
+ 264: Big SAM -> BAM .. ok
+
+ 265: Big SAM -> BAM (2 threads) .. ok
+
+ 266: Big SAM -> BAM (4 threads) .. ok
+
+ 267: Big SAM -> CRAM .. ok
+
+ 268: Big SAM -> CRAM (2 threads) .. ok
+
+ 269: Big SAM -> CRAM (4 threads) .. ok
+
+ 270: Subsample 0.2 (SAM input) ............ ok
+
+ 271: Subsample 0.5 (SAM input) ............ ok
+
+ 272: Subsample 0.8 (SAM input) ............ ok
+
+ 273: Subsample 0.2 (BAM input) ............ ok
+
+ 274: Subsample 0.5 (BAM input) ............ ok
+
+ 275: Subsample 0.8 (BAM input) ............ ok
+
+ 276: Subsample 0.2 (CRAM input) ............ ok
+
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file .. ok
+
+Unsorted mode enabled
+ Generate CRAM file .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/pUOoPqG2pH/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/pUOoPqG2pH/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/pUOoPqG2pH/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/pUOoPqG2pH/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. 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/729OaulfUa - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. 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
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a
+ install -d debian/samtools
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabi/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/arm-linux-gnueabi/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_armel.deb'.
+ dpkg-genchanges -B -marmel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org> >../samtools_1.2-3_armel.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20150922-1632
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_armel.changes:
+─────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: armel
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: armel Build Daemon (antheil) <buildd_armel-antheil at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ 319ccd3f70bf5ea9a2213301128fcc69223b5bc4 336184 samtools_1.2-3_armel.deb
+Checksums-Sha256:
+ e30044dd64712620c208ff4c0039b4cf65b760c97b469f88b2ba5f11d57b2171 336184 samtools_1.2-3_armel.deb
+Files:
+ 0558d5438222c9a2c4208ae15337b658 336184 science optional samtools_1.2-3_armel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_armel.deb
+────────────────────────
+
+ new debian package, version 2.0.
+ size 336184 bytes: control archive=1484 bytes.
+ 802 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: armel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 967
+ Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/bin/
+-rwxr-xr-x root/root 17864 2015-09-22 16:32 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9656 2015-09-22 16:32 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9656 2015-09-22 16:32 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13752 2015-09-22 16:32 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9628 2015-09-22 16:32 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 715032 2015-09-22 16:32 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22020 2015-09-22 16:32 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 16:32 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 16:32 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: armel
+Build-Space: 14816
+Build-Time: 732
+Distribution: sid
+Host Architecture: armel
+Install-Time: 40
+Job: samtools_1.2-3
+Machine Architecture: armel
+Package: samtools
+Package-Time: 896
+Source-Version: 1.2-3
+Space: 14816
+Status: successful
+Version: 1.2-3
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20150922-1632
+Build needed 00:14:56, 14816k disc space
+Signature with key '08BE2BFD' requested:
+ signfile /home/buildd/build/samtools_1.2-3_armel.changes 08BE2BFD
+
+Successfully signed changes file
diff --git a/armhf.log b/armhf.log
deleted file mode 100644
index f1ffbb6..0000000
--- a/armhf.log
+++ /dev/null
@@ -1,898 +0,0 @@
-From buildd at hummel.debian.org Sat Mar 30 09:23:12 2013
-Return-path: <buildd at hummel.debian.org>
-Received: from mailly.debian.org ([82.195.75.114])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at hummel.debian.org>)
- id 1ULs0G-0003ZL-28
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:23:12 +0000
-Received: from hummel.ynic.york.ac.uk ([144.32.168.76] helo=hummel.debian.org)
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=hummel.debian.org, EMAIL=hostmaster at hummel.debian.org (verified)
- by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at hummel.debian.org>)
- id 1ULs0F-0003N1-4a
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:23:11 +0000
-Received: from buildd by hummel.debian.org with local (Exim 4.80)
- (envelope-from <buildd at hummel.debian.org>)
- id 1ULs0B-0003dF-Qb; Sat, 30 Mar 2013 09:23:08 +0000
-From: buildd on hummel <buildd at hummel.debian.org>
-To: logs at buildd.debian.org,buildd-porters at hummel.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on armhf (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Message-Id: <E1ULs0B-0003dF-Qb at hummel.debian.org>
-Date: Sat, 30 Mar 2013 09:23:07 +0000
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on hummel.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (armhf) 30 Mar 2013 09:12 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: armhf
-Get:1 http://ftp.uk.debian.org unstable InRelease [236 kB]
-Get:2 http://incoming.debian.org unstable InRelease [236 kB]
-Get:3 http://ftp.uk.debian.org unstable/main Sources [6484 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:5 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:6 http://ftp.uk.debian.org unstable/contrib Sources [51.0 kB]
-Get:7 http://ftp.uk.debian.org unstable/non-free Sources [101 kB]
-Get:8 http://ftp.uk.debian.org unstable/main armhf Packages [6081 kB]
-Get:9 http://ftp.uk.debian.org unstable/contrib armhf Packages [34.8 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:12 http://incoming.debian.org unstable/main armhf Packages [6081 kB]
-Get:13 http://incoming.debian.org unstable/contrib armhf Packages [34.8 kB]
-Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:17 http://incoming.debian.org buildd-unstable/main armhf Packages [13.1 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib armhf Packages [14 B]
-Fetched 26.1 MB in 1min 33s (279 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (328 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-17)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 22 not upgraded.
-Need to get 9700 kB of archives.
-After this operation, 26.2 MB of additional disk space will be used.
-Get:1 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 armhf 1.2.2-2 [33.7 kB]
-Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base armhf 1.22.2-1 [678 kB]
-Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils armhf 9.0.4 [205 kB]
-Get:4 http://ftp.uk.debian.org/debian/ unstable/main man-db armhf 2.6.3-3 [870 kB]
-Get:5 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp.uk.debian.org/debian/ unstable/main libasprintf0c2 armhf 0.18.1.1-10 [26.8 kB]
-Get:7 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 armhf 1:5.11-2.1 [199 kB]
-Get:8 http://ftp.uk.debian.org/debian/ unstable/main libpcre3 armhf 1:8.31-2 [246 kB]
-Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 armhf 2.8.0+dfsg1-7+nmu1 [785 kB]
-Get:10 http://ftp.uk.debian.org/debian/ unstable/main libffi5 armhf 3.0.10-3+b1 [22.3 kB]
-Get:11 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 armhf 2.33.12+really2.32.4-5 [1709 kB]
-Get:12 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 armhf 0.6.6-2 [120 kB]
-Get:13 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 armhf 0.9.3-5+b1 [404 kB]
-Get:14 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo0 armhf 0.18.1.1-10 [123 kB]
-Get:15 http://ftp.uk.debian.org/debian/ unstable/main file armhf 1:5.11-2.1 [51.5 kB]
-Get:16 http://ftp.uk.debian.org/debian/ unstable/main gettext-base armhf 0.18.1.1-10 [129 kB]
-Get:17 http://ftp.uk.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp.uk.debian.org/debian/ unstable/main html2text armhf 1.3.2a-15+b1 [94.6 kB]
-Get:19 http://ftp.uk.debian.org/debian/ unstable/main libasprintf-dev armhf 0.18.1.1-10 [27.1 kB]
-Get:20 http://ftp.uk.debian.org/debian/ unstable/main libgettextpo-dev armhf 0.18.1.1-10 [143 kB]
-Get:21 http://ftp.uk.debian.org/debian/ unstable/main gettext armhf 0.18.1.1-10 [1706 kB]
-Get:22 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.uk.debian.org/debian/ unstable/main diffstat armhf 1.55-3 [27.5 kB]
-Get:26 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev armhf 5.9-10 [83.9 kB]
-Get:27 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev armhf 5.9-10 [194 kB]
-Get:28 http://ftp.uk.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev armhf 1:1.2.7.dfsg-13 [209 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9700 kB in 3s (2577 kB/s)
-Selecting previously unselected package libpipeline1:armhf.
-(Reading database ... 10833 files and directories currently installed.)
-Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.2-2_armhf.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_armhf.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_armhf.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_armhf.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:armhf.
-Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package libmagic1:armhf.
-Unpacking libmagic1:armhf (from .../libmagic1_1%3a5.11-2.1_armhf.deb) ...
-Selecting previously unselected package libpcre3:armhf.
-Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.31-2_armhf.deb) ...
-Selecting previously unselected package libxml2:armhf.
-Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7+nmu1_armhf.deb) ...
-Selecting previously unselected package libffi5:armhf.
-Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b1_armhf.deb) ...
-Selecting previously unselected package libglib2.0-0:armhf.
-Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.33.12+really2.32.4-5_armhf.deb) ...
-Selecting previously unselected package libcroco3:armhf.
-Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-2_armhf.deb) ...
-Selecting previously unselected package libunistring0:armhf.
-Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5+b1_armhf.deb) ...
-Selecting previously unselected package libgettextpo0:armhf.
-Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_armhf.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_armhf.deb) ...
-Selecting previously unselected package libasprintf-dev:armhf.
-Unpacking libasprintf-dev:armhf (from .../libasprintf-dev_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package libgettextpo-dev:armhf.
-Unpacking libgettextpo-dev:armhf (from .../libgettextpo-dev_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_armhf.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_armhf.deb) ...
-Selecting previously unselected package libtinfo-dev:armhf.
-Unpacking libtinfo-dev:armhf (from .../libtinfo-dev_5.9-10_armhf.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_armhf.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:armhf.
-Unpacking zlib1g-dev:armhf (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_armhf.deb) ...
-Setting up libpipeline1:armhf (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:armhf (0.18.1.1-10) ...
-Setting up libmagic1:armhf (1:5.11-2.1) ...
-Setting up libpcre3:armhf (1:8.31-2) ...
-Setting up libxml2:armhf (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:armhf (3.0.10-3+b1) ...
-Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:armhf (0.6.6-2) ...
-Setting up libunistring0:armhf (0.9.3-5+b1) ...
-Setting up libgettextpo0:armhf (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libasprintf-dev:armhf (0.18.1.1-10) ...
-Setting up libgettextpo-dev:armhf (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:armhf (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:armhf (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 22 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 3.2.0-4-mx5 armhf (armv7l)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.35-2
-Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5 [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture armhf
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-armhf-D4t91G/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_armhf.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_armhf.deb'.
- dpkg-genchanges -B -marmhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org> >../samtools_0.1.19-1_armhf.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0923
-
-samtools_0.1.19-1_armhf.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: armhf
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: armhf Build Daemon (hummel) <buildd_armhf-hummel at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- e2e44ecdbc2a81cfe3ee7ce42a0114ff22990ded 531712 samtools_0.1.19-1_armhf.deb
- 1f686b97cdc388ea1733e335acf545a3ea858c2b 112002 libbam-dev_0.1.19-1_armhf.deb
-Checksums-Sha256:
- 9e901f8398ac191356eca7f608fb27a308aefdf4389610f866eccc25e81e140f 531712 samtools_0.1.19-1_armhf.deb
- b77b5c68c4cb39d7dd053299a0fb27e5401edee46ee1bd39be580b5f8bd36bfa 112002 libbam-dev_0.1.19-1_armhf.deb
-Files:
- 1562af621276816eecd35a1f9f48b77c 531712 science optional samtools_0.1.19-1_armhf.deb
- 4ebb46893751e2c220950fb1a7d739c2 112002 libdevel optional libbam-dev_0.1.19-1_armhf.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_armhf.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 531712 bytes: control archive=1947 bytes.
- 32 bytes, 1 lines conffiles
- 818 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: armhf
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1047
- Depends: libc6 (>= 2.13-28), libgcc1 (>= 1:4.4.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:22 ./
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/samtools/
--rwxr-xr-x root/root 13832 2013-03-30 09:22 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 117880 2013-03-30 09:22 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 9688 2013-03-30 09:22 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 9716 2013-03-30 09:22 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9720 2013-03-30 09:22 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13892 2013-03-30 09:22 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9720 2013-03-30 09:22 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/bin/
--rwxr-xr-x root/root 275848 2013-03-30 09:22 ./usr/bin/samtools
--rwxr-xr-x root/root 100460 2013-03-30 09:22 ./usr/bin/bcftools
--rwxr-xr-x root/root 18064 2013-03-30 09:22 ./usr/bin/razip
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 5778 2013-03-30 09:22 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126580 2013-03-30 09:22 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 1966 2013-03-30 09:22 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/man/man1/
--rw-r--r-- root/root 10654 2013-03-30 09:22 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2013-03-30 09:22 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:22 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_armhf.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 112002 bytes: control archive=930 bytes.
- 712 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: armhf
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 311
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/include/samtools/
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/lib/
--rw-r--r-- root/root 196386 2013-03-30 09:22 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:22 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-armhf-sbuild-fe467231-1b43-413f-a5bb-24c4c3455418/build/buildd-samtools_0.1.19-1-armhf-D4t91G
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: armhf
-Build-Space: 11024
-Build-Time: 372
-Distribution: sid
-Install-Time: 114
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 612
-Source-Version: 0.1.19-1
-Space: 11024
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0923
-Build needed 00:10:12, 11024k disc space
-Signature with key '630B2C7A' requested:
-
diff --git a/hurd-i386.log b/hurd-i386.log
deleted file mode 100644
index 39f3b8a..0000000
--- a/hurd-i386.log
+++ /dev/null
@@ -1,973 +0,0 @@
-From buildd at ironforge.sceen.net Sat Mar 30 09:19:59 2013
-Return-path: <buildd at ironforge.sceen.net>
-Received: from ironforge.sceen.net ([46.105.42.111])
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at ironforge.sceen.net>)
- id 1ULrx9-0002xO-FI
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:59 +0000
-Received: from buildd by ironforge.sceen.net with local (Exim 4.80)
- (envelope-from <buildd at ironforge.sceen.net>)
- id 1ULrxD-0003sk-CG; Sat, 30 Mar 2013 10:20:03 +0100
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.027 (F2.82; B3.13; Q3.13)
-Date: Sat, 30 Mar 2013 10:20:03 +0100
-From: Build Daemon <buildd at ironforge.sceen.net>
-To: samuel.thibault at ens-lyon.org, mbanck at gmx.net, logs at buildd.debian.org,
- debian-hurd-build-logs at lists.alioth.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on hurd-i386 (dist=sid)
-Message-Id: <E1ULrxD-0003sk-CG at ironforge.sceen.net>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on ironforge.sceen.net
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (hurd-i386) 30 Mar 2013 10:16 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: hurd-i386
-Ign file: ./ Release.gpg
-Ign file: ./ Release
-Ign file: ./ Translation-en
-Get:1 http://ftp.fr.debian.org sid Release.gpg [836 B]
-Get:2 http://ftp.fr.debian.org sid Release [235 kB]
-Get:3 http://incoming.debian.org sid Release.gpg [836 B]
-Get:4 http://ftp.fr.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:5 http://incoming.debian.org buildd-sid Release.gpg [836 B]
-Get:6 http://ftp.fr.debian.org sid/contrib Sources/DiffIndex [7819 B]
-Hit http://ftp.fr.debian.org sid/non-free Sources/DiffIndex
-Get:7 http://ftp.fr.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
-Get:8 http://incoming.debian.org sid Release [235 kB]
-Hit http://ftp.fr.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://ftp.fr.debian.org sid/contrib Translation-en/DiffIndex
-Get:9 http://ftp.fr.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:10 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:11 http://ftp.fr.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:12 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:13 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
-Get:14 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:15 http://incoming.debian.org buildd-sid Release [109 kB]
-Get:16 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:17 http://incoming.debian.org sid/contrib Sources/DiffIndex [7819 B]
-Hit http://incoming.debian.org sid/non-free Sources/DiffIndex
-Get:18 http://incoming.debian.org sid/main hurd-i386 Packages/DiffIndex [7876 B]
-Hit http://incoming.debian.org sid/contrib hurd-i386 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
-Get:19 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:20 http://incoming.debian.org buildd-sid/main Sources [11.2 kB]
-Get:21 http://incoming.debian.org buildd-sid/contrib Sources [761 B]
-Get:22 http://incoming.debian.org buildd-sid/non-free Sources [14 B]
-Get:23 http://incoming.debian.org buildd-sid/main hurd-i386 Packages [13.9 kB]
-Get:24 http://incoming.debian.org buildd-sid/contrib hurd-i386 Packages [14 B]
-Get:25 http://ftp.fr.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:26 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
-Get:27 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:28 http://incoming.debian.org buildd-sid/contrib Translation-en [402 B]
-Get:29 http://incoming.debian.org buildd-sid/main Translation-en [13.6 kB]
-Get:30 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:31 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:32 http://incoming.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
-Get:33 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:34 http://ftp.fr.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:35 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
-Get:36 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:37 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:38 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:39 http://ftp.fr.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:40 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:41 http://incoming.debian.org sid/main hurd-i386 2013-03-29-2012.39.pdiff [1577 B]
-Get:42 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:43 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:44 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
-Get:45 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
-Get:46 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:47 http://ftp.fr.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:48 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
-Get:49 http://ftp.fr.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:50 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:51 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0212.50.pdiff [4976 B]
-Get:52 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:53 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:54 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
-Get:55 http://ftp.fr.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
-Get:56 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:57 http://incoming.debian.org sid/main hurd-i386 2013-03-30-0812.16.pdiff [239 B]
-Fetched 716 kB in 1min 15s (9441 B/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-sid/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 2s (244 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
- libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
- man-db
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser groff-base libboost-iostreams1.46.1 libboost-iostreams1.49.0
- libcwidget3 libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
- man-db
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, hurd, libc-bin, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc0.3-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), hurd-dev, debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.2)
-dash: already installed (0.5.7-3+b1)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-hurd: already installed (20120710-3)
-libc-bin: already installed (2.13-37)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-18)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-22)
-sysvinit-utils: already installed (2.88dsf-22)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc0.3-dev: already installed (2.13-37)
-gcc: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.7.2-1 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2+b1)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-hurd-dev: already installed (20120710-3)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: already installed (1:2.0-1)
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
- libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
-Use 'apt-get autoremove' to remove them.
-The following extra packages will be installed:
- diffstat file gettext gettext-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo-dev libgettextpo0
- libglib2.0-0 libmagic1 libtinfo-dev libunistring0 libxml2 po-debconf
-Suggested packages:
- devscripts dh-make gettext-doc ncurses-doc libmail-box-perl procmail
- graphviz default-mta mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- libmail-sendmail-perl less
-The following NEW packages will be installed:
- cdbs debhelper diffstat file gettext gettext-base html2text intltool-debian
- libasprintf-dev libasprintf0c2 libcroco3 libexpat1 libffi5 libgettextpo-dev
- libgettextpo0 libglib2.0-0 libmagic1 libncurses5-dev libtinfo-dev
- libunistring0 libxml2 po-debconf quilt zlib1g-dev
-0 upgraded, 24 newly installed, 0 to remove and 20 not upgraded.
-Need to get 0 B/8015 kB of archives.
-After this operation, 22.7 MB of additional disk space will be used.
-WARNING: The following packages cannot be authenticated!
- libasprintf0c2 libmagic1 libxml2 libffi5 libglib2.0-0 libcroco3 libexpat1
- libunistring0 libgettextpo0 file gettext-base cdbs html2text libasprintf-dev
- libgettextpo-dev gettext intltool-debian po-debconf debhelper diffstat
- libtinfo-dev libncurses5-dev quilt zlib1g-dev
-Authentication warning overridden.
-Selecting previously unselected package libasprintf0c2:hurd-i386.
-(Reading database ... 15400 files and directories currently installed.)
-Unpacking libasprintf0c2:hurd-i386 (from .../libasprintf0c2_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package libmagic1:hurd-i386.
-Unpacking libmagic1:hurd-i386 (from .../libmagic1_1%3a5.11-2.1_hurd-i386.deb) ...
-Selecting previously unselected package libxml2:hurd-i386.
-Unpacking libxml2:hurd-i386 (from .../libxml2_2.8.0+dfsg1-7+nmu1_hurd-i386.deb) ...
-Selecting previously unselected package libffi5:hurd-i386.
-Unpacking libffi5:hurd-i386 (from .../libffi5_3.0.10-3+b1_hurd-i386.deb) ...
-Selecting previously unselected package libglib2.0-0:hurd-i386.
-Unpacking libglib2.0-0:hurd-i386 (from .../libglib2.0-0_2.33.12+really2.32.4-5_hurd-i386.deb) ...
-Selecting previously unselected package libcroco3:hurd-i386.
-Unpacking libcroco3:hurd-i386 (from .../libcroco3_0.6.6-2_hurd-i386.deb) ...
-Selecting previously unselected package libexpat1:hurd-i386.
-Unpacking libexpat1:hurd-i386 (from .../libexpat1_2.1.0-1+b1_hurd-i386.deb) ...
-Selecting previously unselected package libunistring0:hurd-i386.
-Unpacking libunistring0:hurd-i386 (from .../libunistring0_0.9.3-5+b1_hurd-i386.deb) ...
-Selecting previously unselected package libgettextpo0:hurd-i386.
-Unpacking libgettextpo0:hurd-i386 (from .../libgettextpo0_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_hurd-i386.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b2_hurd-i386.deb) ...
-Selecting previously unselected package libasprintf-dev:hurd-i386.
-Unpacking libasprintf-dev:hurd-i386 (from .../libasprintf-dev_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package libgettextpo-dev:hurd-i386.
-Unpacking libgettextpo-dev:hurd-i386 (from .../libgettextpo-dev_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_hurd-i386.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_hurd-i386.deb) ...
-Selecting previously unselected package libtinfo-dev:hurd-i386.
-Unpacking libtinfo-dev:hurd-i386 (from .../libtinfo-dev_5.9-10_hurd-i386.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_hurd-i386.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:hurd-i386.
-Unpacking zlib1g-dev:hurd-i386 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_hurd-i386.deb) ...
-Processing triggers for man-db ...
-Setting up libasprintf0c2:hurd-i386 (0.18.1.1-10) ...
-Setting up libmagic1:hurd-i386 (1:5.11-2.1) ...
-Setting up libxml2:hurd-i386 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:hurd-i386 (3.0.10-3+b1) ...
-Setting up libglib2.0-0:hurd-i386 (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:hurd-i386 (0.6.6-2) ...
-Setting up libexpat1:hurd-i386 (2.1.0-1+b1) ...
-Setting up libunistring0:hurd-i386 (0.9.3-5+b1) ...
-Setting up libgettextpo0:hurd-i386 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15+b2) ...
-Setting up libasprintf-dev:hurd-i386 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:hurd-i386 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:hurd-i386 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:hurd-i386 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
- libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Checking correctness of dependencies...
-Kernel: GNU 0.3 hurd-i386 (i686-AT386)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.7_4.7.2-5 gcc-4.7_4.7.2-5 gnumach-dev_2:1.3.99.dfsg.git20130311-1 hurd-dev_20120710-3 libc0.3-dev_2.13-37 libstdc++6_4.7.2-5 libstdc++6-4.7-dev_4.7.2-5
-Package versions: adduser_3.113+nmu3 apt_0.9.7.8 apt-utils_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpio_2.11+dfsg-0.1 cpp_4:4.7.2-1 cpp-4.7_4.7.2-5 dash_0.5.7-3+b1 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debian-ports-archive-keyring_2012.12.30 debianutils_4.3.4 diffstat_1.55-3 di [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture hurd-i386
- /usr/bin/fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/bcftools'
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c: In function 'MD5Final':
-md5.c:149:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-md5.c:150:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- /usr/bin/fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_hurd-i386.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_hurd-i386.deb'.
- dpkg-genchanges -B -mDebian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org> >../samtools_0.1.19-1_hurd-i386.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-1019
-
-samtools_0.1.19-1_hurd-i386.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: hurd-i386
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: Debian GNU/Hurd Build Daemon <buildd_hurd-i386-ironforge at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- b08658b3ebb58880b3f2e0fe86f4a0279da4e7da 564414 samtools_0.1.19-1_hurd-i386.deb
- 3320893118fbf04bfb6a1b61dd8487d1c795868d 127000 libbam-dev_0.1.19-1_hurd-i386.deb
-Checksums-Sha256:
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- 6d688ddc590c100fda7a17206b556490645fcd6fb79cb7f4e4fd58c0f61abbcd 127000 libbam-dev_0.1.19-1_hurd-i386.deb
-Files:
- 8dfb78cd74823389be6e73ee9a9fa3c3 564414 science optional samtools_0.1.19-1_hurd-i386.deb
- eed5c18c1ca603a33a80c6a5ff08b1f5 127000 libdevel optional libbam-dev_0.1.19-1_hurd-i386.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_hurd-i386.deb
-───────────────────────────────
-
- new debian package, version 2.0.
- size 564414 bytes: control archive= 1942 bytes.
- 32 bytes, 1 lines conffiles
- 802 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1351
- Depends: libc0.3 (>= 2.13-37), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 10:19 ./
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 15:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 03:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 03:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 08:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 10:19 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 15:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 15:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 15:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 15:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 15:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 10:19 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 09:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 10:19 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 10:19 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 15:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 15:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 15:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 15:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 15:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 15:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 15:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 15:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 15:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 15:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 15:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 15:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 10:19 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 15:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 15:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 15:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/bin/
--rwxr-xr-x root/root 157732 2013-03-30 10:19 ./usr/bin/bcftools
--rwxr-xr-x root/root 26152 2013-03-30 10:19 ./usr/bin/razip
--rwxr-xr-x root/root 439700 2013-03-30 10:19 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/samtools/
--rwxr-xr-x root/root 17896 2013-03-30 10:19 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 17840 2013-03-30 10:19 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 187448 2013-03-30 10:19 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 9628 2013-03-30 10:19 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9628 2013-03-30 10:19 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 13728 2013-03-30 10:19 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 9604 2013-03-30 10:19 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 23:52 ./etc/bash_completion.d/samtools
-lrwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_hurd-i386.deb
-─────────────────────────────────
-
- new debian package, version 2.0.
- size 127000 bytes: control archive= 927 bytes.
- 716 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: hurd-i386
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 405
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 15:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 08:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 15:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 09:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/lib/
--rw-r--r-- root/root 292396 2013-03-30 10:19 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 10:19 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 15:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 15:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 15:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 15:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 15:43 ./usr/include/samtools/sam.h
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /home/buildd/build/chroot-sid/build/buildd-samtools_0.1.19-1-hurd-i386-N0JuSS
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
- libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
-Use 'apt-get autoremove' to remove them.
-0 upgraded, 0 newly installed, 0 to remove and 20 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages were automatically installed and are no longer required:
- adduser libboost-iostreams1.46.1 libboost-iostreams1.49.0 libcwidget3
- libpopt0 libsigc++-2.0-0c2a libssl1.0.0 libsysfs2 libxapian22
-Use 'apt-get autoremove' to remove them.
-The following packages will be REMOVED:
- cdbs* debhelper* diffstat* file* gettext* gettext-base* html2text*
- intltool-debian* libasprintf-dev* libasprintf0c2* libcroco3* libexpat1*
- libffi5* libgettextpo-dev* libgettextpo0* libglib2.0-0* libmagic1*
- libncurses5-dev* libtinfo-dev* libunistring0* libxml2* po-debconf* quilt*
- zlib1g-dev*
-0 upgraded, 0 newly installed, 24 to remove and 20 not upgraded.
-After this operation, 22.7 MB disk space will be freed.
-(Reading database ... 16504 files and directories currently installed.)
-Removing cdbs ...
-Removing debhelper ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libasprintf-dev:hurd-i386 ...
-Removing libasprintf0c2:hurd-i386 ...
-Removing libcroco3:hurd-i386 ...
-Purging configuration files for libcroco3:hurd-i386 ...
-Removing libexpat1:hurd-i386 ...
-Purging configuration files for libexpat1:hurd-i386 ...
-Removing libglib2.0-0:hurd-i386 ...
-Purging configuration files for libglib2.0-0:hurd-i386 ...
-Removing libffi5:hurd-i386 ...
-Purging configuration files for libffi5:hurd-i386 ...
-Removing libgettextpo-dev:hurd-i386 ...
-Removing libgettextpo0:hurd-i386 ...
-Removing libmagic1:hurd-i386 ...
-Purging configuration files for libmagic1:hurd-i386 ...
-Removing libncurses5-dev ...
-Removing libtinfo-dev:hurd-i386 ...
-Removing libunistring0:hurd-i386 ...
-Purging configuration files for libunistring0:hurd-i386 ...
-Removing libxml2:hurd-i386 ...
-Purging configuration files for libxml2:hurd-i386 ...
-Removing zlib1g-dev:hurd-i386 ...
-Processing triggers for man-db ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: hurd-i386
-Build-Space: 13640
-Build-Time: 88
-Distribution: sid
-Install-Time: 18
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 194
-Source-Version: 0.1.19-1
-Space: 13640
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-1019
-Build needed 00:03:14, 13640k disc space
diff --git a/i386.log b/i386.log
index 626d5f2..6409da5 100644
--- a/i386.log
+++ b/i386.log
@@ -1,74 +1,45 @@
-From buildd at brahms.debian.org Thu Sep 25 00:27:27 2014
-Return-path: <buildd at brahms.debian.org>
-Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at brahms.debian.org>)
- id 1XWwu7-0007j9-7F
- for logs at buildd.debian.org; Thu, 25 Sep 2014 00:27:27 +0000
-Received: from brahms.debian.org ([2607:f8f0:610:4000:216:36ff:fe40:3802])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=brahms.debian.org, EMAIL=hostmaster at brahms.debian.org (verified)
- by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at brahms.debian.org>)
- id 1XWwu6-0004pk-By
- for logs at buildd.debian.org; Thu, 25 Sep 2014 00:27:26 +0000
-Received: from buildd by brahms.debian.org with local (Exim 4.80)
- (envelope-from <buildd at brahms.debian.org>)
- id 1XWwu4-0005ih-Eq; Thu, 25 Sep 2014 00:27:24 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 00:27:24 +0000
-From: buildd on brahms <buildd at brahms.debian.org>
-To: buildd-admin at brahms.debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_1.1-1 on i386 (dist=sid)
-Key-Id: 4C7A7FBE
-Message-Id: <E1XWwu4-0005ih-Eq at brahms.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on brahms.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on x86-csail-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (i386) 25 Sep 2014 00:24 ║
+║ samtools 1.2-3 (i386) 22 Sep 2015 16:06 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
Machine Architecture: amd64
Host Architecture: i386
Build Architecture: i386
-I: NOTICE: Log filtering will replace 'build/samtools-YjmHXD/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-YjmHXD' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-813c0d07-75a0-43f9-aa37-749f9218ed0c' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-Et2_7Z/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-Et2_7Z' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-i386-sbuild-1cb31428-a4ec-4cce-8d40-8cfe912fabad' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
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-Fetched 30.7 MB in 19s (1542 kB/s)
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+Get:11 http://debian.csail.mit.edu unstable/non-free Sources [106 kB]
+Get:12 http://debian.csail.mit.edu unstable/main i386 Packages [7549 kB]
+Get:13 http://debian.csail.mit.edu unstable/contrib i386 Packages [57.8 kB]
+Get:14 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:17 http://ftp.debian.org unstable/main i386 Packages [7549 kB]
+Get:18 http://ftp.debian.org unstable/contrib i386 Packages [57.8 kB]
+Fetched 32.8 MB in 11s (2913 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 6s (693 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 0s (24.1 MB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-oiP7_X/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-A798Xu/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -116,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 29 not upgraded.
-Need to get 0 B/818 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/774 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10660 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-qL3kk0/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11918 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-Sw8sPU/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -140,185 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
- libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
- zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 25 newly installed, 0 to remove and 26 not upgraded.
-Need to get 11.0 MB/11.0 MB of archives.
-After this operation, 31.9 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin i386 5.9+20140913-1 [348 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 i386 5.9+20140913-1 [282 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 i386 5.9+20140913-1 [103 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 i386 1.3.1-1 [27.6 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base i386 1.22.2-8 [1167 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils i386 9.0.5 [207 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db i386 2.7.0.1-1 [1008 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 i386 0.19.2-2 [30.9 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 i386 1:5.19-2 [242 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 i386 2.9.1+dfsg1-4 [828 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 i386 3.1-2 [17.9 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 i386 2.42.0-1 [2545 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 i386 0.6.8-3 [141 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 i386 1.1-1 [215 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 i386 0.9.3-5.2 [284 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file i386 1:5.19-2 [58.0 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base i386 0.19.2-2 [121 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext i386 0.19.2-2 [1243 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev i386 1.1-1 [255 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev i386 5.9+20140913-1 [76.0 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev i386 5.9+20140913-1 [177 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix i386 1.1-1 [197 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev i386 1:1.2.8.dfsg-2 [205 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 18.5 MB/18.5 MB of archives.
+After this operation, 65.2 MB of additional disk space will be used.
+Get:1 http://debian.csail.mit.edu/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://debian.csail.mit.edu/debian/ unstable/main groff-base i386 1.22.3-1 [1174 kB]
+Get:3 http://debian.csail.mit.edu/debian/ unstable/main bsdmainutils i386 9.0.6 [183 kB]
+Get:4 http://debian.csail.mit.edu/debian/ unstable/main libpipeline1 i386 1.4.1-1 [29.8 kB]
+Get:5 http://debian.csail.mit.edu/debian/ unstable/main man-db i386 2.7.3-1 [1011 kB]
+Get:6 http://debian.csail.mit.edu/debian/ unstable/main libffi6 i386 3.2.1-3 [19.2 kB]
+Get:7 http://debian.csail.mit.edu/debian/ unstable/main libglib2.0-0 i386 2.44.1-1.1 [2522 kB]
+Get:8 http://debian.csail.mit.edu/debian/ unstable/main libicu55 i386 55.1-5 [7762 kB]
+Get:9 http://debian.csail.mit.edu/debian/ unstable/main libxml2 i386 2.9.2+zdfsg1-4 [945 kB]
+Get:10 http://debian.csail.mit.edu/debian/ unstable/main libcroco3 i386 0.6.8-3+b1 [141 kB]
+Get:11 http://debian.csail.mit.edu/debian/ unstable/main libunistring0 i386 0.9.3-5.2+b1 [288 kB]
+Get:12 http://debian.csail.mit.edu/debian/ unstable/main libmagic1 i386 1:5.25-1 [261 kB]
+Get:13 http://debian.csail.mit.edu/debian/ unstable/main file i386 1:5.25-1 [61.4 kB]
+Get:14 http://debian.csail.mit.edu/debian/ unstable/main gettext-base i386 0.19.6-1 [123 kB]
+Get:15 http://debian.csail.mit.edu/debian/ unstable/main gettext i386 0.19.6-1 [1473 kB]
+Get:16 http://debian.csail.mit.edu/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://debian.csail.mit.edu/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://debian.csail.mit.edu/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://debian.csail.mit.edu/debian/ unstable/main libhts1 i386 1.2.1-1 [240 kB]
+Get:20 http://debian.csail.mit.edu/debian/ unstable/main libhts-dev i386 1.2.1-1 [283 kB]
+Get:21 http://debian.csail.mit.edu/debian/ unstable/main libio-pty-perl i386 1:1.08-1+b4 [36.4 kB]
+Get:22 http://debian.csail.mit.edu/debian/ unstable/main libtinfo-dev i386 6.0+20150810-1 [76.5 kB]
+Get:23 http://debian.csail.mit.edu/debian/ unstable/main libncurses5-dev i386 6.0+20150810-1 [174 kB]
+Get:24 http://debian.csail.mit.edu/debian/ unstable/main tabix i386 1.2.1-1 [230 kB]
+Get:25 http://debian.csail.mit.edu/debian/ unstable/main zlib1g-dev i386 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 11.0 MB in 1s (6462 kB/s)
-(Reading database ... 10660 files and directories currently installed.)
-Preparing to unpack .../ncurses-bin_5.9+20140913-1_i386.deb ...
-Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up ncurses-bin (5.9+20140913-1) ...
-(Reading database ... 10660 files and directories currently installed.)
-Preparing to unpack .../libtinfo5_5.9+20140913-1_i386.deb ...
-Unpacking libtinfo5:i386 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libtinfo5:i386 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-11) ...
-(Reading database ... 10660 files and directories currently installed.)
-Preparing to unpack .../libncurses5_5.9+20140913-1_i386.deb ...
-Unpacking libncurses5:i386 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libncurses5:i386 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-11) ...
-Selecting previously unselected package libpipeline1:i386.
-(Reading database ... 10660 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_i386.deb ...
-Unpacking libpipeline1:i386 (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_i386.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5_i386.deb ...
-Unpacking bsdmainutils (9.0.5) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_i386.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:i386.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_i386.deb ...
-Unpacking libasprintf0c2:i386 (0.19.2-2) ...
-Selecting previously unselected package libmagic1:i386.
-Preparing to unpack .../libmagic1_1%3a5.19-2_i386.deb ...
-Unpacking libmagic1:i386 (1:5.19-2) ...
-Selecting previously unselected package libxml2:i386.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4_i386.deb ...
-Unpacking libxml2:i386 (2.9.1+dfsg1-4) ...
-Selecting previously unselected package libffi6:i386.
-Preparing to unpack .../libffi6_3.1-2_i386.deb ...
-Unpacking libffi6:i386 (3.1-2) ...
-Selecting previously unselected package libglib2.0-0:i386.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_i386.deb ...
-Unpacking libglib2.0-0:i386 (2.42.0-1) ...
-Selecting previously unselected package libcroco3:i386.
-Preparing to unpack .../libcroco3_0.6.8-3_i386.deb ...
-Unpacking libcroco3:i386 (0.6.8-3) ...
-Selecting previously unselected package libhts1:i386.
-Preparing to unpack .../libhts1_1.1-1_i386.deb ...
-Unpacking libhts1:i386 (1.1-1) ...
-Selecting previously unselected package libunistring0:i386.
-Preparing to unpack .../libunistring0_0.9.3-5.2_i386.deb ...
-Unpacking libunistring0:i386 (0.9.3-5.2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_i386.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_i386.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_i386.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:i386.
-Preparing to unpack .../libhts-dev_1.1-1_i386.deb ...
-Unpacking libhts-dev:i386 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:i386.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_i386.deb ...
-Unpacking libtinfo-dev:i386 (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:i386.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_i386.deb ...
-Unpacking libncurses5-dev:i386 (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../archives/tabix_1.1-1_i386.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:i386.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_i386.deb ...
-Unpacking zlib1g-dev:i386 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:i386 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:i386 (0.19.2-2) ...
-Setting up libmagic1:i386 (1:5.19-2) ...
-Setting up libxml2:i386 (2.9.1+dfsg1-4) ...
-Setting up libffi6:i386 (3.1-2) ...
-Setting up libglib2.0-0:i386 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:i386 (0.6.8-3) ...
-Setting up libhts1:i386 (1.1-1) ...
-Setting up libunistring0:i386 (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:i386 (1.1-1) ...
-Setting up libtinfo-dev:i386 (5.9+20140913-1) ...
-Setting up libncurses5-dev:i386 (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Fetched 18.5 MB in 1s (18.4 MB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 11918 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_i386.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_i386.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:i386.
+Preparing to unpack .../libpipeline1_1.4.1-1_i386.deb ...
+Unpacking libpipeline1:i386 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_i386.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:i386.
+Preparing to unpack .../libffi6_3.2.1-3_i386.deb ...
+Unpacking libffi6:i386 (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:i386.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_i386.deb ...
+Unpacking libglib2.0-0:i386 (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:i386.
+Preparing to unpack .../libicu55_55.1-5_i386.deb ...
+Unpacking libicu55:i386 (55.1-5) ...
+Selecting previously unselected package libxml2:i386.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_i386.deb ...
+Unpacking libxml2:i386 (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:i386.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_i386.deb ...
+Unpacking libcroco3:i386 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:i386.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_i386.deb ...
+Unpacking libunistring0:i386 (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:i386.
+Preparing to unpack .../libmagic1_1%3a5.25-1_i386.deb ...
+Unpacking libmagic1:i386 (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_i386.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_i386.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_i386.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:i386.
+Preparing to unpack .../libhts1_1.2.1-1_i386.deb ...
+Unpacking libhts1:i386 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:i386.
+Preparing to unpack .../libhts-dev_1.2.1-1_i386.deb ...
+Unpacking libhts-dev:i386 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:i386.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_i386.deb ...
+Unpacking libtinfo-dev:i386 (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:i386.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_i386.deb ...
+Unpacking libncurses5-dev:i386 (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_i386.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:i386 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:i386 (3.2.1-3) ...
+Setting up libglib2.0-0:i386 (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:i386 (55.1-5) ...
+Setting up libxml2:i386 (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:i386 (0.6.8-3+b1) ...
+Setting up libunistring0:i386 (0.9.3-5.2+b1) ...
+Setting up libmagic1:i386 (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:i386 (1.2.1-1) ...
+Setting up libhts-dev:i386 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:i386 (6.0+20150810-1) ...
+Setting up libncurses5-dev:i386 (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:i386 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.2.0-4-amd64 amd64 (x86_64)
-Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-14 gcc-4.9_4.9.1-14 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-14 libstdc++6_4.9.1-14 linux-libc-dev_3.16.2-3
-Package versions: apt_1.0.8 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-14 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4 [...]
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -329,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -348,7 +317,7 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=2
+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
@@ -357,7 +326,7 @@ SCHROOT_CHROOT_NAME=sid-i386-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-i386-sbuild-813c0d07-75a0-43f9-aa37-749f9218ed0c
+SCHROOT_SESSION_ID=sid-i386-sbuild-1cb31428-a4ec-4cce-8d40-8cfe912fabad
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -367,16 +336,16 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture i386
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
- make -j2 distclean
+ make -j4 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
@@ -391,9 +360,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -414,7 +385,7 @@ dh_auto_build -- \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
@@ -430,8 +401,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -440,10 +410,6 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
-padding.c: In function 'bam_pad2unpad':
-padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
- fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
@@ -462,10 +428,6 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
-misc/ace2sam.c: In function 'main':
-misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
- fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
@@ -476,15 +438,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
-test/merge/test_rtrans_build.c: In function 'main':
-test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMIC_SEED = 0x1234abcd330e;
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
-test/merge/test_trans_tbl_init.c: In function 'main':
-test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMMICK_SEED = 0x1234abcd330e;
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
@@ -492,6 +446,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
@@ -505,9 +460,9 @@ gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_tran
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-linux-gnu/libhts.a -lhts -lcurses [...]
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-linux-gnu/libhts.a -lhts -lcurses -lm -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -516,251 +471,265 @@ dh_auto_test -- \
HTSDIR="/usr/include" \
HTSLIB=/usr/lib/i386-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/PHZ6a904Ap/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/drlgpH3C_c/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/PHZ6a904Ap/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/drlgpH3C_c/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/PHZ6a904Ap/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/drlgpH3C_c/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/PHZ6a904Ap/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/drlgpH3C_c/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/PHZ6a904Ap/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/drlgpH3C_c/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/PHZ6a904Ap/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/drlgpH3C_c/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/PHZ6a904Ap/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/drlgpH3C_c/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/PHZ6a904Ap/mpileup.bam.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/drlgpH3C_c/mpileup.bam.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/PHZ6a904Ap/mpileup.bam.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/drlgpH3C_c/mpileup.bam.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/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/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/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/PHZ6a904Ap/mpileup.cram.list -f /tmp/PHZ6a904Ap/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/drlgpH3C_c/mpileup.cram.list -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:1050-1060 /tmp/PHZ6a904Ap/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:1050-1060 /tmp/drlgpH3C_c/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/PHZ6a904Ap/mpileup.ref.fa.gz -r17:1050-1060 /tmp/PHZ6a904Ap/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/drlgpH3C_c/mpileup.ref.fa.gz -r17:1050-1060 /tmp/drlgpH3C_c/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
-test_view:
- Generating test data file .................. done
- 1: SAM -> BAM -> SAM
- SAM files differ at /tmp/PHZ6a904Ap/view.test001.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test001.bam -b /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test001.bam.sam /tmp/PHZ6a904Ap/view.test001.bam
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+test_usage_subcommand:
+ samtools faidx
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 2: SAM -> uncompressed BAM .. ok
+test_usage_subcommand:
+ samtools index
+.. ok
- 3: uncompressed BAM -> SAM and compare
- SAM files differ at /tmp/PHZ6a904Ap/view.test003.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test003.sam -h /tmp/PHZ6a904Ap/view.test002.bam
+test_usage_subcommand:
+ samtools calmd
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools fixmate
+.. ok
- 4: SAM -> fast compressed BAM .. ok
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
- 5: fast compressed BAM -> SAM and compare
- SAM files differ at /tmp/PHZ6a904Ap/view.test005.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test005.sam -h /tmp/PHZ6a904Ap/view.test004.bam
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools bamshuf
- 6: SAM -> CRAM -> SAM (UR header tags)
- SAM files differ at /tmp/PHZ6a904Ap/view.test006.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test006.cram -C /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test006.cram.sam /tmp/PHZ6a904Ap/view.test006.cram
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools cat
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
- 7: SAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/PHZ6a904Ap/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test007.cram.sam /tmp/PHZ6a904Ap/view.test007.cram
+test_usage_subcommand:
+ samtools mpileup
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools sort
+.. ok
- 8: BAM -> CRAM with UR -> SAM
- SAM files differ at /tmp/PHZ6a904Ap/view.test008.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test008.cram -C /tmp/PHZ6a904Ap/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test008.cram.sam /tmp/PHZ6a904Ap/view.test008.cram
+test_usage_subcommand:
+ samtools split
+.. ok
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
-.. failed ...
+test_usage_subcommand:
+ samtools bedcov
- 9: SAM -> BAM (M5 header tags)
- SAM files differ at /tmp/PHZ6a904Ap/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test009.bam.sam /tmp/PHZ6a904Ap/view.test009.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools depth
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/PHZ6a904Ap/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test010.cram -C /tmp/PHZ6a904Ap/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test010.cram.sam /tmp/PHZ6a904Ap/view.test010.cram
+test_usage_subcommand:
+ samtools flagstat
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools idxstats
- 11: CRAM -> BAM with UR
- SAM files differ at /tmp/PHZ6a904Ap/view.test011.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test011.bam -b /tmp/PHZ6a904Ap/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test011.bam.sam /tmp/PHZ6a904Ap/view.test011.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools phase
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 12: CRAM -> BAM with M5
- SAM files differ at /tmp/PHZ6a904Ap/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test012.bam -b /tmp/PHZ6a904Ap/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test012.bam.sam /tmp/PHZ6a904Ap/view.test012.bam
+test_usage_subcommand:
+ samtools stats
+.. ok
+test_usage_subcommand:
+ samtools flags
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 13: SAM -> SAM via stdout
- SAM files differ at /tmp/PHZ6a904Ap/view.test013.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/view.001.sam
+test_usage_subcommand:
+ samtools tview
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools view
- 14: SAM -> BAM via stdout .. ok
+ Usage on stderr rather than stdout
+.. expected failure
- 15: SAM -> CRAM via stdout
- SAM files differ at /tmp/PHZ6a904Ap/view.test015.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -C /tmp/PHZ6a904Ap/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test015.cram.sam /tmp/PHZ6a904Ap/view.test015.cram
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+ 2: SAM -> uncompressed BAM .. ok
-.. failed ...
+ 3: uncompressed BAM -> SAM and compare .. ok
- 16: SAM from stdin -> SAM
- SAM files differ at /tmp/PHZ6a904Ap/view.test016.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test016.sam -h -
+ 4: SAM -> fast compressed BAM .. ok
+ 5: fast compressed BAM -> SAM and compare .. ok
-.. failed ...
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
- 17: BAM from stdin -> SAM
- SAM files differ at /tmp/PHZ6a904Ap/view.test017.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test017.sam -h -
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
+ 8: BAM -> CRAM with UR -> SAM .. ok
-.. failed ...
+ 9: SAM -> BAM (M5 header tags) .. ok
- 18: CRAM from stdin -> SAM
- SAM files differ at /tmp/PHZ6a904Ap/view.test018.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test018.sam -h -
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
+ 11: CRAM -> BAM with UR .. ok
-.. failed ...
+ 12: CRAM -> BAM with M5 .. ok
- 19: samtools view -H (SAM input) .. ok
+ 13: SAM -> SAM via stdout .. ok
- 20: samtools view -H (BAM input) .. ok
+ 14: SAM -> BAM via stdout .. ok
- 21: samtools view -H (CRAM input) .. ok
+ 15: SAM -> CRAM via stdout .. ok
- 22: No headers (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test022.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test022.body /tmp/PHZ6a904Ap/view.001.sam
+ 16: SAM from stdin -> SAM .. ok
+ 17: BAM from stdin -> SAM .. ok
-.. failed ...
+ 18: CRAM from stdin -> SAM .. ok
- 23: No headers (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test023.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test023.body /tmp/PHZ6a904Ap/view.test001.bam
+ 19: samtools view -H (SAM input) .. ok
+ 20: samtools view -H (BAM input) .. ok
-.. failed ...
+ 21: samtools view -H (CRAM input) .. ok
- 24: No headers (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test024.body : 6 / /tmp/PHZ6a904Ap/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test024.body /tmp/PHZ6a904Ap/view.test006.cram
+ 22: No headers (SAM input) .. ok
+ 23: No headers (BAM input) .. ok
-.. failed ...
+ 24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
@@ -774,206 +743,116 @@ test_view:
30: Count -f 128 (CRAM input) .. ok
- 31: Filter -F 128 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test031.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test031.sam -h -F 128 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
- 33: Filter -F 128 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test033.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test033.sam -h -F 128 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
- 35: Filter -F 128 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test035.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test035.sam -h -F 128 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
- 37: Filter -F 128 -f 2 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test037.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test037.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/PHZ6a904Ap/view.test039.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test039.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/PHZ6a904Ap/view.test041.sam : 34 / /tmp/PHZ6a904Ap/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test041.sam -h -F 128 -f 2 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
- 43: Filter -r grp2 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test043.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test043.sam -h -r grp2 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
- 45: Filter -r grp2 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test045.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test045.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
- 47: Filter -r grp2 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test047.sam : 29 / /tmp/PHZ6a904Ap/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test047.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/drlgpH3C_c/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input) .. ok
+ 50: Count -R /tmp/drlgpH3C_c/view.001.fogn (SAM input) .. ok
- 52: Count -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/drlgpH3C_c/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input) .. ok
+ 52: Count -R /tmp/drlgpH3C_c/view.001.fogn (BAM input) .. ok
- 54: Count -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test055.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test055.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.001.sam
+ 54: Count -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input) .. ok
+ 55: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (SAM input).. ok
-.. failed ...
+ 56: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (SAM input).. ok
+ 57: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (BAM input).. ok
- 57: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test057.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test057.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
+ 58: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (BAM input).. ok
+ 59: Filter -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (CRAM input).. ok
-.. failed ...
+ 60: Count -R /tmp/drlgpH3C_c/view.001.fogn -r grp2 (CRAM input).. ok
- 58: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (BAM input).. ok
+ 61: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (SAM input).. ok
- 59: Filter -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test059.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test059.sam -h -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
+ 62: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (SAM input).. ok
+ 63: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (BAM input).. ok
-.. failed ...
+ 64: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (BAM input).. ok
- 60: Count -R /tmp/PHZ6a904Ap/view.001.fogn -r grp2 (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test061.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test061.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
-
- 62: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (SAM input).. ok
-
- 63: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test063.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test063.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
-
- 64: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (BAM input).. ok
-
- 65: Filter -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test065.sam : 34 / /tmp/PHZ6a904Ap/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test065.sam -h -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
-
- 66: Count -r grp2 -R /tmp/PHZ6a904Ap/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/drlgpH3C_c/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test067.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/drlgpH3C_c/view.test067.sam -h -l Library 2 /tmp/drlgpH3C_c/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/drlgpH3C_c/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test069.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/drlgpH3C_c/view.test069.sam -h -l Library 2 /tmp/drlgpH3C_c/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/drlgpH3C_c/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test071.sam -h -l Library 2 /tmp/PHZ6a904Ap/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/drlgpH3C_c/view.test071.sam -h -l Library 2 /tmp/drlgpH3C_c/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/PHZ6a904Ap/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/drlgpH3C_c/view.test006.cram
.. expected failure
@@ -1014,153 +893,63 @@ Samtools-htslib-API: bam_get_library() not yet implemented
90: Count -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test091.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test091.sam -h -x fa /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 91: Filter -x fa (SAM input) .. ok
92: Count -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test093.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test093.sam -h -x fa /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 93: Filter -x fa (BAM input) .. ok
94: Count -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test095.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test095.sam -h -x fa /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 95: Filter -x fa (CRAM input) .. ok
96: Count -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test097.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test097.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 97: Filter -x fa -x ha (SAM input) .. ok
98: Count -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test099.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test099.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 99: Filter -x fa -x ha (BAM input) .. ok
100: Count -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test101.sam : 34 / /tmp/PHZ6a904Ap/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test101.sam -h -x fa -x ha /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 101: Filter -x fa -x ha (CRAM input) .. ok
102: Count -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test103.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test103.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
104: Count -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test105.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test105.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
106: Count -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test107.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test107.sam -h -x fa -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
108: Count -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test109.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test109.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
110: Count -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test111.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test111.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
112: Count -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test113.sam : 29 / /tmp/PHZ6a904Ap/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test113.sam -h -x RG -r grp2 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
114: Count -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test115.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test115.sam -h -m 10 /tmp/PHZ6a904Ap/view.001.sam
-
-
-.. failed ...
+ 115: Filter -m 10 (SAM input) .. ok
116: Count -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test117.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test117.sam -h -m 10 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 117: Filter -m 10 (BAM input) .. ok
118: Count -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test119.sam : 34 / /tmp/PHZ6a904Ap/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test119.sam -h -m 10 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 119: Filter -m 10 (CRAM input) .. ok
120: Count -m 10 (CRAM input) .. ok
@@ -1228,143 +1017,59 @@ Samtools-htslib-API: bam_get_library() not yet implemented
151: Count Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test152.sam : 34 / /tmp/PHZ6a904Ap/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test152.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1
-
-
-.. failed ...
+ 152: Region ref1 (BAM input) .. ok
153: Count ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test154.sam : 34 / /tmp/PHZ6a904Ap/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test154.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1
-
-
-.. failed ...
+ 154: Region ref1 (CRAM input) .. ok
155: Count ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test156.sam : 31 / /tmp/PHZ6a904Ap/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test156.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15
-
-
-.. failed ...
+ 156: Region ref1:15 (BAM input) .. ok
157: Count ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test158.sam : 31 / /tmp/PHZ6a904Ap/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test158.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15
-
-
-.. failed ...
+ 158: Region ref1:15 (CRAM input) .. ok
159: Count ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test160.sam : 31 / /tmp/PHZ6a904Ap/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test160.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 160: Region ref1:15-45 (BAM input) .. ok
161: Count ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test162.sam : 31 / /tmp/PHZ6a904Ap/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test162.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 162: Region ref1:15-45 (CRAM input) .. ok
163: Count ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test164.sam : 31 / /tmp/PHZ6a904Ap/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test164.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2
-
-
-.. failed ...
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
165: Count ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test166.sam : 31 / /tmp/PHZ6a904Ap/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test166.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2
-
-
-.. failed ...
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
167: Count ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test168.sam : 31 / /tmp/PHZ6a904Ap/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test168.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2:16
-
-
-.. failed ...
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
169: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test170.sam : 31 / /tmp/PHZ6a904Ap/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test170.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2:16
-
-
-.. failed ...
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test172.sam : 31 / /tmp/PHZ6a904Ap/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test172.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test174.sam : 31 / /tmp/PHZ6a904Ap/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test174.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test176.sam : 31 / /tmp/PHZ6a904Ap/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test176.sam -h /tmp/PHZ6a904Ap/view.test001.bam ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test178.sam : 31 / /tmp/PHZ6a904Ap/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test178.sam -h /tmp/PHZ6a904Ap/view.test006.cram ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
@@ -1384,23 +1089,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
187: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test188.sam : 28 / /tmp/PHZ6a904Ap/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test188.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
189: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test190.sam : 28 / /tmp/PHZ6a904Ap/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test190.sam -h -r grp2 /tmp/PHZ6a904Ap/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
@@ -1420,43 +1113,19 @@ Samtools-htslib-API: bam_get_library() not yet implemented
199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test200.sam : 33 / /tmp/PHZ6a904Ap/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 200: 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
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test202.sam : 33 / /tmp/PHZ6a904Ap/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 202: 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
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test204.sam : 34 / /tmp/PHZ6a904Ap/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 204: 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
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test206.sam : 34 / /tmp/PHZ6a904Ap/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 206: 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
@@ -1492,23 +1161,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
223: 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)
- SAM files differ at /tmp/PHZ6a904Ap/view.test224.sam : 33 / /tmp/PHZ6a904Ap/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test001.bam ref1:11-16
-
-
-.. failed ...
+ 224: 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
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test226.sam : 33 / /tmp/PHZ6a904Ap/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/PHZ6a904Ap/view.test006.cram ref1:11-16
-
-
-.. failed ...
+ 226: 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
@@ -1536,23 +1193,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
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 -q 5 (BAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test240.sam : 29 / /tmp/PHZ6a904Ap/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/PHZ6a904Ap/view.test001.bam
-
-
-.. failed ...
+ 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 -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
- SAM files differ at /tmp/PHZ6a904Ap/view.test242.sam : 29 / /tmp/PHZ6a904Ap/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/PHZ6a904Ap/view.test006.cram
-
-
-.. failed ...
+ 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 -q 5 (CRAM input).. ok
@@ -1564,141 +1209,67 @@ Samtools-htslib-API: bam_get_library() not yet implemented
247: 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
- SAM files differ at /tmp/PHZ6a904Ap/view.001.no_sq.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.001.no_sq.bam -b /tmp/PHZ6a904Ap/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.001.no_sq.bam.sam /tmp/PHZ6a904Ap/view.001.no_sq.bam
-
-
-.. failed ...
-
- 249: Add @SQ with -t (SAM -> SAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test249.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam
-
-
-.. failed ...
-
- 250: Add @SQ with -T (SAM -> SAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test250.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam
-
-
-.. failed ...
-
- 251: Add @SQ with -t (BAM -> SAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test251.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam
-
-
-.. failed ...
+ 248: Make BAM with no M5/UR tags .. ok
- 252: Add @SQ with -T (BAM -> SAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test252.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
-.. failed ...
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test253.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test253.bam.sam /tmp/PHZ6a904Ap/view.test253.bam
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
-.. failed ...
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test254.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test254.bam.sam /tmp/PHZ6a904Ap/view.test254.bam
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
-.. failed ...
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test255.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test255.bam.sam /tmp/PHZ6a904Ap/view.test255.bam
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
-.. failed ...
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test256.bam.sam : 34 / /tmp/PHZ6a904Ap/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test256.bam.sam /tmp/PHZ6a904Ap/view.test256.bam
+ 261: Make CRAM with no UR field .. ok
+ 262: Decoding CRAM with no UR field via -T .. ok
-.. failed ...
+ 263: CIGAR B-operator removal .. ok
- 257: Add @SQ with -t (SAM -> CRAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test257.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test257.cram.sam /tmp/PHZ6a904Ap/view.test257.cram
+ 264: Big SAM -> BAM .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
-.. failed ...
+ 266: Big SAM -> BAM (4 threads) .. ok
- 258: Add @SQ with -T (SAM -> CRAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test258.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test258.cram.sam /tmp/PHZ6a904Ap/view.test258.cram
+ 267: Big SAM -> CRAM .. ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
-.. failed ...
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 259: Add @SQ with -t (BAM -> CRAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test259.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test259.cram.sam /tmp/PHZ6a904Ap/view.test259.cram
+ 270: Subsample 0.2 (SAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
-.. failed ...
+ 272: Subsample 0.8 (SAM input) ............ ok
- 260: Add @SQ with -T (BAM -> CRAM)
- SAM files differ at /tmp/PHZ6a904Ap/view.test260.cram.sam : 34 / /tmp/PHZ6a904Ap/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/PHZ6a904Ap/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/PHZ6a904Ap/view.test260.cram.sam /tmp/PHZ6a904Ap/view.test260.cram
+ 273: Subsample 0.2 (BAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
-.. failed ...
+ 275: Subsample 0.8 (BAM input) ............ ok
- 261: CIGAR B-operator removal .. ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
- 262: Big SAM -> BAM .. ok
+ 277: Subsample 0.5 (CRAM input) ............ ok
- 263: Big SAM -> BAM (2 threads) .. ok
-
- 264: Big SAM -> BAM (4 threads) .. ok
-
- 265: Big SAM -> CRAM .. ok
-
- 266: Big SAM -> CRAM (2 threads) .. ok
-
- 267: Big SAM -> CRAM (4 threads) .. ok
-
- 268: Subsample 0.2 (SAM input) ............ ok
-
- 269: Subsample 0.5 (SAM input) ............ ok
-
- 270: Subsample 0.8 (SAM input) ............ ok
-
- 271: Subsample 0.2 (BAM input) ............ ok
-
- 272: Subsample 0.5 (BAM input) ............ ok
-
- 273: Subsample 0.8 (BAM input) ............ ok
-
- 274: Subsample 0.2 (CRAM input) ............ ok
-
- 275: Subsample 0.5 (CRAM input) ............ ok
-
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1726,21 +1297,10 @@ test_cat:
6: cat recompressed BAM files with new header .. ok
test_bam2fq:
- Generate BAM file
- SAM files differ at GLOB(0x940eafc) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/bam2fq.001.bam
-
-
-.. failed ...
-
- Generate CRAM file
- SAM files differ at GLOB(0x95099f4) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/PHZ6a904Ap/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/PHZ6a904Ap/bam2fq.001.cram
-
+ Generate BAM file .. ok
-.. failed ...
+Unsorted mode enabled
+ Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
1: bam2fq (SAM input) .. ok
@@ -1793,28 +1353,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/PHZ6a904Ap/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/drlgpH3C_c/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/PHZ6a904Ap/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/drlgpH3C_c/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/PHZ6a904Ap/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/drlgpH3C_c/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/PHZ6a904Ap/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/drlgpH3C_c/depad.001p.bam
.. expected failure
@@ -1845,16 +1405,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 21899 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/V6s2T3YPb4
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/tf0f5Fk0ku - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/LYZcGZxZrg - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1888,29 +1446,257 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 237
- failed .. 87
- expected failure .. 18
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
unexpected pass .. 0
-make[2]: *** [test] Error 1
-Makefile:183: recipe for target 'test' failed
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
make[2]: Leaving directory '/«PKGBUILDDIR»'
-dh_auto_test: make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
-make[1]: *** [override_dh_auto_test] Error 2
-make: *** [build-arch] Error 2
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
-debian/rules:18: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
-debian/rules:6: recipe for target 'build-arch' failed
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-linux-gnu/libhts.a
+ install -d debian/samtools
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/i386-linux-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/i386-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_i386.deb'.
+ dpkg-genchanges -B -mamd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org> >../samtools_1.2-3_i386.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0027
+Build finished at 20150922-1608
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_i386.changes:
+────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: i386
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: amd64 / i386 Build Daemon (x86-csail-01) <buildd_amd64-x86-csail-01 at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ 97c12ab7015984dfe7c3e0faf2a039c00b9e2cde 407944 samtools_1.2-3_i386.deb
+Checksums-Sha256:
+ e8d7b5d48c3dd064e6a12ba055e456aa4d518920e9262fc38cee065f3c56f221 407944 samtools_1.2-3_i386.deb
+Files:
+ c2b8bbf29c4c95809d739ba42bc3839d 407944 science optional samtools_1.2-3_i386.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_i386.deb
+───────────────────────
+
+ new debian package, version 2.0.
+ size 407944 bytes: control archive=1483 bytes.
+ 802 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: i386
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1111
+ Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/bin/
+-rwxr-xr-x root/root 17812 2015-09-22 16:08 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9600 2015-09-22 16:08 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9600 2015-09-22 16:08 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13696 2015-09-22 16:08 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9572 2015-09-22 16:08 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 866564 2015-09-22 16:08 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17872 2015-09-22 16:08 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 16:08 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 16:08 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1924,20 +1710,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: i386
-Build-Space: 20484
-Build-Time: 98
+Build-Space: 15080
+Build-Time: 83
Distribution: sid
-Fail-Stage: build
Host Architecture: i386
-Install-Time: 38
-Job: samtools_1.1-1
+Install-Time: 11
+Job: samtools_1.2-3
Machine Architecture: amd64
Package: samtools
-Package-Time: 186
-Source-Version: 1.1-1
-Space: 20484
-Status: attempted
-Version: 1.1-1
+Package-Time: 117
+Source-Version: 1.2-3
+Space: 15080
+Status: successful
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0027
-Build needed 00:03:06, 20484k disc space
+Finished at 20150922-1608
+Build needed 00:01:57, 15080k disc space
+Signature with key 'F5E1965F' requested:
+ signfile /home/buildd/build/samtools_1.2-3_i386.changes F5E1965F
+
+Successfully signed changes file
diff --git a/ia64.log b/ia64.log
deleted file mode 100644
index d2cc210..0000000
--- a/ia64.log
+++ /dev/null
@@ -1,958 +0,0 @@
-From buildd at caballero.debian.org Sat Mar 30 09:19:15 2013
-Return-path: <buildd at caballero.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1ULrwR-0002tw-J9
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:15 +0000
-Received: from caballero.debian.org ([193.201.200.200])
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- EMAIL=hostmaster at caballero.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at caballero.debian.org>)
- id 1ULrwP-0001bN-Dq; Sat, 30 Mar 2013 09:19:13 +0000
-Received: from buildd by caballero.debian.org with local (Exim 4.72)
- (envelope-from <buildd at caballero.debian.org>) id 1ULrwO-0000hZ-5g
- for buildd-porters at caballero.debian.org; Sat, 30 Mar 2013 09:19:12 +0000
-Date: Sat, 30 Mar 2013 09:19:12 +0000
-Message-Id: <E1ULrwO-0000hZ-5g at caballero.debian.org>
-From: buildd on caballero <buildd at caballero.debian.org>
-To: buildd-porters at caballero.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on ia64 (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: buildd-porters at caballero.debian.org
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on caballero.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (ia64) 30 Mar 2013 09:14 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: ia64
-Get:1 http://ftp.uk.debian.org sid InRelease [236 kB]
-Get:2 http://ftp.uk.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:3 http://incoming.debian.org sid InRelease [236 kB]
-Get:4 http://ftp.uk.debian.org sid/contrib Sources/DiffIndex [7819 B]
-Get:5 http://ftp.uk.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
-Ign http://incoming.debian.org InRelease
-Hit http://ftp.uk.debian.org sid/contrib ia64 Packages/DiffIndex
-Hit http://ftp.uk.debian.org sid/contrib Translation-en/DiffIndex
-Get:6 http://ftp.uk.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:7 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:8 http://incoming.debian.org Release.gpg [836 B]
-Get:9 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:10 http://ftp.uk.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:11 http://ftp.uk.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
-Get:12 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:13 http://incoming.debian.org sid/main Sources/DiffIndex [7876 B]
-Get:14 http://incoming.debian.org sid/contrib Sources/DiffIndex [7819 B]
-Get:15 http://incoming.debian.org sid/main ia64 Packages/DiffIndex [7876 B]
-Hit http://incoming.debian.org sid/contrib ia64 Packages/DiffIndex
-Hit http://incoming.debian.org sid/contrib Translation-en/DiffIndex
-Get:16 http://incoming.debian.org sid/main Translation-en/DiffIndex [7876 B]
-Get:17 http://incoming.debian.org Release [1141 B]
-Get:18 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:19 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:20 http://incoming.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
-Get:21 http://ftp.uk.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:22 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:23 http://ftp.uk.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
-Get:24 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:25 http://incoming.debian.org Sources [12.5 kB]
-Get:26 http://incoming.debian.org Packages [98.1 kB]
-Ign http://incoming.debian.org Translation-en
-Get:27 http://ftp.uk.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:28 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
-Get:29 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [4869 B]
-Get:30 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:31 http://incoming.debian.org sid/contrib 2013-03-30-0212.50.pdiff [386 B]
-Get:32 http://incoming.debian.org sid/main ia64 2013-03-29-2012.39.pdiff [788 B]
-Get:33 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:34 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:35 http://incoming.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
-Get:36 http://incoming.debian.org sid/main 2013-03-29-2012.39.pdiff [694 B]
-Get:37 http://ftp.uk.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:38 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
-Get:39 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:40 http://ftp.uk.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:41 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
-Get:42 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [1972 B]
-Get:43 http://incoming.debian.org sid/main ia64 2013-03-30-0212.50.pdiff [5004 B]
-Get:44 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:45 http://ftp.uk.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:46 http://incoming.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
-Get:47 http://incoming.debian.org sid/main 2013-03-30-0212.50.pdiff [33 B]
-Get:48 http://ftp.uk.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
-Get:49 http://incoming.debian.org sid/main 2013-03-30-0812.16.pdiff [857 B]
-Get:50 http://incoming.debian.org sid/main ia64 2013-03-30-0812.16.pdiff [484 B]
-Fetched 678 kB in 37s (17.9 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (486 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6.1-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.2)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6.1-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 29 newly installed, 0 to remove and 12 not upgraded.
-Need to get 0 B/11.6 MB of archives.
-After this operation, 39.0 MB of additional disk space will be used.
-Selecting previously unselected package libpipeline1:ia64.
-(Reading database ... 10657 files and directories currently installed.)
-Unpacking libpipeline1:ia64 (from .../libpipeline1_1.2.2-2_ia64.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_ia64.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_ia64.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_ia64.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:ia64.
-Unpacking libasprintf0c2:ia64 (from .../libasprintf0c2_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package libmagic1:ia64.
-Unpacking libmagic1:ia64 (from .../libmagic1_1%3a5.11-2.1_ia64.deb) ...
-Selecting previously unselected package libpcre3:ia64.
-Unpacking libpcre3:ia64 (from .../libpcre3_1%3a8.31-2_ia64.deb) ...
-Selecting previously unselected package libxml2:ia64.
-Unpacking libxml2:ia64 (from .../libxml2_2.8.0+dfsg1-7+nmu1_ia64.deb) ...
-Selecting previously unselected package libffi5:ia64.
-Unpacking libffi5:ia64 (from .../libffi5_3.0.10-3_ia64.deb) ...
-Selecting previously unselected package libglib2.0-0:ia64.
-Unpacking libglib2.0-0:ia64 (from .../libglib2.0-0_2.33.12+really2.32.4-5_ia64.deb) ...
-Selecting previously unselected package libcroco3:ia64.
-Unpacking libcroco3:ia64 (from .../libcroco3_0.6.6-2_ia64.deb) ...
-Selecting previously unselected package libunistring0:ia64.
-Unpacking libunistring0:ia64 (from .../libunistring0_0.9.3-5_ia64.deb) ...
-Selecting previously unselected package libgettextpo0:ia64.
-Unpacking libgettextpo0:ia64 (from .../libgettextpo0_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_ia64.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_ia64.deb) ...
-Selecting previously unselected package libasprintf-dev:ia64.
-Unpacking libasprintf-dev:ia64 (from .../libasprintf-dev_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package libgettextpo-dev:ia64.
-Unpacking libgettextpo-dev:ia64 (from .../libgettextpo-dev_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_ia64.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_ia64.deb) ...
-Selecting previously unselected package libtinfo-dev:ia64.
-Unpacking libtinfo-dev:ia64 (from .../libtinfo-dev_5.9-10_ia64.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_ia64.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:ia64.
-Unpacking zlib1g-dev:ia64 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_ia64.deb) ...
-Setting up libpipeline1:ia64 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:ia64 (0.18.1.1-10) ...
-Setting up libmagic1:ia64 (1:5.11-2.1) ...
-Setting up libpcre3:ia64 (1:8.31-2) ...
-Setting up libxml2:ia64 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:ia64 (3.0.10-3) ...
-Setting up libglib2.0-0:ia64 (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:ia64 (0.6.6-2) ...
-Setting up libunistring0:ia64 (0.9.3-5) ...
-Setting up libgettextpo0:ia64 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:ia64 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:ia64 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:ia64 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:ia64 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-bpo.5-mckinley ia64 (ia64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6.1-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.35-2
-Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 file_1:5.11-2.1 [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture ia64
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-ia64-lETMhD/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_ia64.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_ia64.deb'.
- dpkg-genchanges -B -mia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org> >../samtools_0.1.19-1_ia64.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0919
-
-samtools_0.1.19-1_ia64.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: ia64
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: ia64 Build Daemon (caballero) <buildd_ia64-caballero at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 08231110072e321aadf0bb616b84902899cb6f85 649304 samtools_0.1.19-1_ia64.deb
- 260c83972875780dcadc914e1c2e4fd7e1f76055 162484 libbam-dev_0.1.19-1_ia64.deb
-Checksums-Sha256:
- d4aee74d03a41f6b111de6daf7a8b0a98e670aa00546784cd7f8d7485da2d7d5 649304 samtools_0.1.19-1_ia64.deb
- 82809e9a2dbf9b3f814506bece9b63079ca9dd2bf580139efbe6463eadacbb59 162484 libbam-dev_0.1.19-1_ia64.deb
-Files:
- be183fa863a5afe3f488d229c29ceb7d 649304 science optional samtools_0.1.19-1_ia64.deb
- 9d9068029d621e4507e82e9ee0d06b38 162484 libdevel optional libbam-dev_0.1.19-1_ia64.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_ia64.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 649304 bytes: control archive= 1935 bytes.
- 32 bytes, 1 lines conffiles
- 793 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 2268
- Depends: libc6.1 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:18 ./
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:18 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 09:18 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:18 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:18 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:18 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/bin/
--rwxr-xr-x root/root 355552 2013-03-30 09:18 ./usr/bin/bcftools
--rwxr-xr-x root/root 50912 2013-03-30 09:18 ./usr/bin/razip
--rwxr-xr-x root/root 911304 2013-03-30 09:18 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/samtools/
--rwxr-xr-x root/root 31264 2013-03-30 09:18 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 37152 2013-03-30 09:18 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 378512 2013-03-30 09:18 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 13200 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13200 2013-03-30 09:18 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 22400 2013-03-30 09:18 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 15072 2013-03-30 09:18 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:18 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_ia64.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 162484 bytes: control archive= 923 bytes.
- 711 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: ia64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 680
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/lib/
--rw-r--r-- root/root 573810 2013-03-30 09:18 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:18 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-ia64-sbuild-d68654b1-c4f1-4be0-bbbc-6fab61321d58/build/buildd-samtools_0.1.19-1-ia64-lETMhD
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 12 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
- gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
- libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
- libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 29 to remove and 12 not upgraded.
-After this operation, 39.0 MB disk space will be freed.
-(Reading database ... 12825 files and directories currently installed.)
-Removing bash-completion ...
-Purging configuration files for bash-completion ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing cdbs ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libasprintf-dev:ia64 ...
-Removing libasprintf0c2:ia64 ...
-Removing libcroco3:ia64 ...
-Purging configuration files for libcroco3:ia64 ...
-Removing libglib2.0-0:ia64 ...
-Purging configuration files for libglib2.0-0:ia64 ...
-Removing libffi5:ia64 ...
-Purging configuration files for libffi5:ia64 ...
-Removing libgettextpo-dev:ia64 ...
-Removing libgettextpo0:ia64 ...
-Removing libmagic1:ia64 ...
-Purging configuration files for libmagic1:ia64 ...
-Removing libncurses5-dev ...
-Removing libpcre3:ia64 ...
-Purging configuration files for libpcre3:ia64 ...
-Removing libpipeline1:ia64 ...
-Purging configuration files for libpipeline1:ia64 ...
-Removing libtinfo-dev:ia64 ...
-Removing libunistring0:ia64 ...
-Purging configuration files for libunistring0:ia64 ...
-Removing libxml2:ia64 ...
-Purging configuration files for libxml2:ia64 ...
-Removing zlib1g-dev:ia64 ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: ia64
-Build-Space: 18476
-Build-Time: 162
-Distribution: sid
-Install-Time: 30
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 243
-Source-Version: 0.1.19-1
-Space: 18476
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0919
-Build needed 00:04:03, 18476k disc space
-
diff --git a/kfreebsd-amd64.log b/kfreebsd-amd64.log
index 9c57b14..f16fdcf 100644
--- a/kfreebsd-amd64.log
+++ b/kfreebsd-amd64.log
@@ -1,74 +1,45 @@
-From buildd at fano.debian.org Thu Sep 25 00:31:28 2014
-Return-path: <buildd at fano.debian.org>
-Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
- id 1XWwy0-0007ye-EG
- for logs at buildd.debian.org; Thu, 25 Sep 2014 00:31:28 +0000
-Received: from fano.debian.org ([2607:f8f0:610:4000:6564:a62:19:110])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
- id 1XWwxy-0005aW-Mh; Thu, 25 Sep 2014 00:31:26 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.80)
- (envelope-from <buildd at fano.debian.org>)
- id 1XWwxx-000Ir4-Vn; Thu, 25 Sep 2014 00:31:26 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 00:31:25 +0000
-From: buildd on fano <buildd at fano.debian.org>
-To: christoph at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_1.1-1 on kfreebsd-amd64
- (dist=sid)
-Key-Id: 8C5D26F3
-Message-Id: <E1XWwxx-000Ir4-Vn at fano.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on fano.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fano.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (kfreebsd-amd64) 25 Sep 2014 00:27 ║
+║ samtools 1.2-3 (kfreebsd-amd64) 22 Sep 2015 17:23 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
Machine Architecture: kfreebsd-amd64
Host Architecture: kfreebsd-amd64
Build Architecture: kfreebsd-amd64
-I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ka-sbuild-1411604862-68022' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-qWsSJB/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-qWsSJB' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-kfreebsd-amd64-sbuild-1442942612-57690' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
-Get:2 http://mirror-ubc.debian.org unstable/main Sources [9757 kB]
-Get:3 http://ftp.debian.org unstable InRelease [233 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [67.0 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [127 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
-Get:8 http://incoming.debian.org buildd-unstable/main Sources [450 kB]
-Get:9 http://ftp.debian.org unstable/main Sources [9757 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
-Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1082 B]
-Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1643 B]
-Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [336 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [773 B]
-Get:15 http://ftp.debian.org unstable/contrib Sources [67.0 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [127 kB]
-Get:17 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
-Get:18 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
-Fetched 38.7 MB in 12s (3087 kB/s)
+Get:1 http://mirror-ubc.debian.org unstable InRelease [253 kB]
+Get:2 http://mirror-ubc.debian.org unstable/main Sources [8093 kB]
+Get:3 http://ftp.debian.org unstable InRelease [253 kB]
+Get:4 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [59.7 kB]
+Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [106 kB]
+Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [6980 kB]
+Get:8 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [42.6 kB]
+Get:9 http://incoming.debian.org buildd-unstable/main Sources [356 kB]
+Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1252 B]
+Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [84.0 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [1064 B]
+Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:17 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [6980 kB]
+Get:18 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [42.6 kB]
+Fetched 31.6 MB in 13s (2356 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 5s (853 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 4s (1022 kB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-jaSah8/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ytP0Ls/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -116,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 38 not upgraded.
-Need to get 0 B/822 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/776 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-1LN58k/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
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(Reading database ... 40%
(Reading database ... 45%
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11308 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-qlG7Zs/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -140,185 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
- libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
- zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 25 newly installed, 0 to remove and 35 not upgraded.
-Need to get 10.8 MB/10.8 MB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin kfreebsd-amd64 5.9+20140913-1 [347 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-amd64 5.9+20140913-1 [283 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-amd64 5.9+20140913-1 [96.8 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.3.1-1 [26.6 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.2-8 [1050 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.5 [211 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.0.1-1 [995 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.19.2-2 [30.8 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.19-2 [238 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.1+dfsg1-4 [801 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.1-2 [19.3 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.0-1 [2480 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3 [134 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-amd64 1.1-1 [205 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2 [283 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.19-2 [58.2 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.2-2 [120 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.2-2 [1232 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-amd64 1.1-1 [250 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9+20140913-1 [76.7 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9+20140913-1 [173 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-amd64 1.1-1 [190 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2 [206 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 18.0 MB/18.0 MB of archives.
+After this operation, 64.4 MB of additional disk space will be used.
+Get:1 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.3-1 [1077 kB]
+Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.6 [183 kB]
+Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.4.1-1 [28.0 kB]
+Get:5 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.3-1 [997 kB]
+Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.2.1-3 [19.4 kB]
+Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.1-1 [2397 kB]
+Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libicu55 kfreebsd-amd64 55.1-5 [7649 kB]
+Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.2+zdfsg1-4 [888 kB]
+Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3+b1 [135 kB]
+Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2+b1 [287 kB]
+Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.25-1 [255 kB]
+Get:13 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.25-1 [61.6 kB]
+Get:14 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.6-1 [122 kB]
+Get:15 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.6-1 [1457 kB]
+Get:16 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-amd64 1.2.1-1 [229 kB]
+Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-amd64 1.2.1-1 [277 kB]
+Get:21 http://mirror-ubc.debian.org/debian/ unstable/main libio-pty-perl kfreebsd-amd64 1:1.08-1+b4 [36.0 kB]
+Get:22 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 6.0+20150810-1 [77.6 kB]
+Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 6.0+20150810-1 [171 kB]
+Get:24 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-amd64 1.2.1-1 [223 kB]
+Get:25 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2+b1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.8 MB in 0s (15.4 MB/s)
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../ncurses-bin_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up ncurses-bin (5.9+20140913-1) ...
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../libtinfo5_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libtinfo5:kfreebsd-amd64 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libtinfo5:kfreebsd-amd64 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-10) ...
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../libncurses5_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libncurses5:kfreebsd-amd64 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libncurses5:kfreebsd-amd64 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-10) ...
-Selecting previously unselected package libpipeline1:kfreebsd-amd64.
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_kfreebsd-amd64.deb ...
-Unpacking libpipeline1:kfreebsd-amd64 (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_kfreebsd-amd64.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5_kfreebsd-amd64.deb ...
-Unpacking bsdmainutils (9.0.5) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_kfreebsd-amd64.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_kfreebsd-amd64.deb ...
-Unpacking libasprintf0c2:kfreebsd-amd64 (0.19.2-2) ...
-Selecting previously unselected package libmagic1:kfreebsd-amd64.
-Preparing to unpack .../libmagic1_1%3a5.19-2_kfreebsd-amd64.deb ...
-Unpacking libmagic1:kfreebsd-amd64 (1:5.19-2) ...
-Selecting previously unselected package libxml2:kfreebsd-amd64.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4_kfreebsd-amd64.deb ...
-Unpacking libxml2:kfreebsd-amd64 (2.9.1+dfsg1-4) ...
-Selecting previously unselected package libffi6:kfreebsd-amd64.
-Preparing to unpack .../libffi6_3.1-2_kfreebsd-amd64.deb ...
-Unpacking libffi6:kfreebsd-amd64 (3.1-2) ...
-Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_kfreebsd-amd64.deb ...
-Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
-Selecting previously unselected package libcroco3:kfreebsd-amd64.
-Preparing to unpack .../libcroco3_0.6.8-3_kfreebsd-amd64.deb ...
-Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3) ...
-Selecting previously unselected package libhts1:kfreebsd-amd64.
-Preparing to unpack .../libhts1_1.1-1_kfreebsd-amd64.deb ...
-Unpacking libhts1:kfreebsd-amd64 (1.1-1) ...
-Selecting previously unselected package libunistring0:kfreebsd-amd64.
-Preparing to unpack .../libunistring0_0.9.3-5.2_kfreebsd-amd64.deb ...
-Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_kfreebsd-amd64.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_kfreebsd-amd64.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_kfreebsd-amd64.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:kfreebsd-amd64.
-Preparing to unpack .../libhts-dev_1.1-1_kfreebsd-amd64.deb ...
-Unpacking libhts-dev:kfreebsd-amd64 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.1-1_kfreebsd-amd64.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_kfreebsd-amd64.deb ...
-Unpacking zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:kfreebsd-amd64 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:kfreebsd-amd64 (0.19.2-2) ...
-Setting up libmagic1:kfreebsd-amd64 (1:5.19-2) ...
-Setting up libxml2:kfreebsd-amd64 (2.9.1+dfsg1-4) ...
-Setting up libffi6:kfreebsd-amd64 (3.1-2) ...
-Setting up libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-amd64 (0.6.8-3) ...
-Setting up libhts1:kfreebsd-amd64 (1.1-1) ...
-Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:kfreebsd-amd64 (1.1-1) ...
-Setting up libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Setting up libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-10) ...
+Fetched 18.0 MB in 1s (14.6 MB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 30%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11308 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_kfreebsd-amd64.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_kfreebsd-amd64.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:kfreebsd-amd64.
+Preparing to unpack .../libpipeline1_1.4.1-1_kfreebsd-amd64.deb ...
+Unpacking libpipeline1:kfreebsd-amd64 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_kfreebsd-amd64.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:kfreebsd-amd64.
+Preparing to unpack .../libffi6_3.2.1-3_kfreebsd-amd64.deb ...
+Unpacking libffi6:kfreebsd-amd64 (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:kfreebsd-amd64.
+Preparing to unpack .../libglib2.0-0_2.42.1-1_kfreebsd-amd64.deb ...
+Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ...
+Selecting previously unselected package libicu55:kfreebsd-amd64.
+Preparing to unpack .../libicu55_55.1-5_kfreebsd-amd64.deb ...
+Unpacking libicu55:kfreebsd-amd64 (55.1-5) ...
+Selecting previously unselected package libxml2:kfreebsd-amd64.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_kfreebsd-amd64.deb ...
+Unpacking libxml2:kfreebsd-amd64 (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:kfreebsd-amd64.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_kfreebsd-amd64.deb ...
+Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:kfreebsd-amd64.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_kfreebsd-amd64.deb ...
+Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:kfreebsd-amd64.
+Preparing to unpack .../libmagic1_1%3a5.25-1_kfreebsd-amd64.deb ...
+Unpacking libmagic1:kfreebsd-amd64 (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_kfreebsd-amd64.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_kfreebsd-amd64.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_kfreebsd-amd64.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:kfreebsd-amd64.
+Preparing to unpack .../libhts1_1.2.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts1:kfreebsd-amd64 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:kfreebsd-amd64.
+Preparing to unpack .../libhts-dev_1.2.1-1_kfreebsd-amd64.deb ...
+Unpacking libhts-dev:kfreebsd-amd64 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_kfreebsd-amd64.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_kfreebsd-amd64.deb ...
+Unpacking libtinfo-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_kfreebsd-amd64.deb ...
+Unpacking libncurses5-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_kfreebsd-amd64.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:kfreebsd-amd64 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:kfreebsd-amd64 (3.2.1-3) ...
+Setting up libglib2.0-0:kfreebsd-amd64 (2.42.1-1) ...
+No schema files found: doing nothing.
+Setting up libicu55:kfreebsd-amd64 (55.1-5) ...
+Setting up libxml2:kfreebsd-amd64 (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:kfreebsd-amd64 (0.6.8-3+b1) ...
+Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2+b1) ...
+Setting up libmagic1:kfreebsd-amd64 (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:kfreebsd-amd64 (1.2.1-1) ...
+Setting up libhts-dev:kfreebsd-amd64 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Setting up libncurses5-dev:kfreebsd-amd64 (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: GNU/kFreeBSD 9.0-2-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-12 gcc-4.9_4.9.1-12 kfreebsd-kernel-headers_10.0~5 libc0.1-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12
-Package versions: apt_1.0.7 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-12 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4 [...]
+Kernel: GNU/kFreeBSD 10.1-0-amd64 kfreebsd-amd64 (x86_64)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 kfreebsd-kernel-headers_10.1~5 libc0.1-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17
+Package versions: apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-1 findutils_4.4 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -329,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -353,25 +322,26 @@ HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-kfreebsd-amd64-sbuild
-SCHROOT_CHROOT_NAME=sid-ka-sbuild
+SCHROOT_CHROOT_NAME=sid-kfreebsd-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ka-sbuild-1411604862-68022
+SCHROOT_SESSION_ID=sid-kfreebsd-amd64-sbuild-1442942612-57690
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+USERNAME=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture kfreebsd-amd64
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -391,9 +361,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -430,8 +402,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -476,6 +447,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
@@ -491,7 +463,7 @@ gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/tes
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lcu [...]
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lcurses -lm -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -503,91 +475,213 @@ dh_auto_test -- \
make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/hbsGdk3of9/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/hbsGdk3of9/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/hbsGdk3of9/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/hbsGdk3of9/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/2K2PBSgp_6/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/hbsGdk3of9/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/hbsGdk3of9/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/hbsGdk3of9/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/hbsGdk3of9/mpileup.bam.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/hbsGdk3of9/mpileup.bam.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/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/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/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/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/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/hbsGdk3of9/mpileup.cram.list -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hbsGdk3of9/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/hbsGdk3of9/mpileup.ref.fa.gz -r17:1050-1060 /tmp/hbsGdk3of9/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
@@ -686,80 +780,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/hbsGdk3of9/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/hbsGdk3of9/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/hbsGdk3of9/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/hbsGdk3of9/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/hbsGdk3of9/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/hbsGdk3of9/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test067.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/hbsGdk3of9/view.test067.sam -h -l Library 2 /tmp/hbsGdk3of9/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/hbsGdk3of9/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test069.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/hbsGdk3of9/view.test069.sam -h -l Library 2 /tmp/hbsGdk3of9/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/hbsGdk3of9/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test071.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/hbsGdk3of9/view.test071.sam -h -l Library 2 /tmp/hbsGdk3of9/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/hbsGdk3of9/view.test006.cram
.. expected failure
@@ -1142,37 +1236,41 @@ Samtools-htslib-API: bam_get_library() not yet implemented
260: Add @SQ with -T (BAM -> CRAM) .. ok
- 261: CIGAR B-operator removal .. ok
+ 261: Make CRAM with no UR field .. ok
+
+ 262: Decoding CRAM with no UR field via -T .. ok
- 262: Big SAM -> BAM .. ok
+ 263: CIGAR B-operator removal .. ok
- 263: Big SAM -> BAM (2 threads) .. ok
+ 264: Big SAM -> BAM .. ok
- 264: Big SAM -> BAM (4 threads) .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
- 265: Big SAM -> CRAM .. ok
+ 266: Big SAM -> BAM (4 threads) .. ok
- 266: Big SAM -> CRAM (2 threads) .. ok
+ 267: Big SAM -> CRAM .. ok
- 267: Big SAM -> CRAM (4 threads) .. ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
- 268: Subsample 0.2 (SAM input) ............ ok
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 269: Subsample 0.5 (SAM input) ............ ok
+ 270: Subsample 0.2 (SAM input) ............ ok
- 270: Subsample 0.8 (SAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
- 271: Subsample 0.2 (BAM input) ............ ok
+ 272: Subsample 0.8 (SAM input) ............ ok
- 272: Subsample 0.5 (BAM input) ............ ok
+ 273: Subsample 0.2 (BAM input) ............ ok
- 273: Subsample 0.8 (BAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
- 274: Subsample 0.2 (CRAM input) ............ ok
+ 275: Subsample 0.8 (BAM input) ............ ok
- 275: Subsample 0.5 (CRAM input) ............ ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1202,6 +1300,7 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
+Unsorted mode enabled
Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
@@ -1255,28 +1354,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/hbsGdk3of9/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/hbsGdk3of9/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/hbsGdk3of9/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/hbsGdk3of9/depad.001p.bam
.. expected failure
@@ -1307,16 +1406,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 70698 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/j8G9qPU9yq
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qbbLiy2S7U - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/VlizHCAsyu - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1350,10 +1447,10 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 324
+ total .. 368
+ passed .. 336
failed .. 0
- expected failure .. 18
+ expected failure .. 32
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1407,20 +1504,20 @@ make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -a -O--parallel
install -d debian/samtools//usr
- cp -a debian/tmp/usr/bin debian/samtools//usr/
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
- cp -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
dh_installdocs -a -O--parallel
- install -g 0 -o 0 -d debian/samtools/usr/share/doc/samtools
- cp -a AUTHORS debian/samtools/usr/share/doc/samtools
- cp -a debian/reference debian/samtools/usr/share/doc/samtools
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
chown -R 0:0 debian/samtools/usr/share/doc
chmod -R go=rX debian/samtools/usr/share/doc
chmod -R u\+rw debian/samtools/usr/share/doc
- install -g 0 -o 0 -m 644 -p debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
- install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ install -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 -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
@@ -1437,13 +1534,13 @@ make[1]: Leaving directory '/«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 644
- find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
- find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
+ find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
+ find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/lib/x86_64-kfreebsd-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/samtools/usr/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
@@ -1458,31 +1555,32 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
- install -o 0 -g 0 -d debian/samtools/DEBIAN
+ install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/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/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5sum-lite were not linked against libhts.so.1 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
- chmod 644 debian/samtools/DEBIAN/control
+ chmod 0644 debian/samtools/DEBIAN/control
chown 0:0 debian/samtools/DEBIAN/control
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 644 debian/samtools/DEBIAN/md5sums
+ chmod 0644 debian/samtools/DEBIAN/md5sums
chown 0:0 debian/samtools/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb --build debian/samtools ..
-dpkg-deb: building package `samtools' in `../samtools_1.1-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_1.1-1_kfreebsd-amd64.changes
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_kfreebsd-amd64.deb'.
+ dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_1.2-3_kfreebsd-amd64.changes
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.1
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0031
+Build finished at 20150922-1726
Finished
────────
@@ -1499,57 +1597,55 @@ I: Built successfully
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.1-1_kfreebsd-amd64.changes:
+samtools_1.2-3_kfreebsd-amd64.changes:
──────────────────────────────────────
Format: 1.8
-Date: Thu, 25 Sep 2014 09:04:20 +0900
+Date: Tue, 22 Sep 2015 06:42:01 -0700
Source: samtools
Binary: samtools samtools-test
Architecture: kfreebsd-amd64
-Version: 1.1-1
+Version: 1.2-3
Distribution: sid
Urgency: medium
Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package.
+Closes: 799698
Changes:
- samtools (1.1-1) unstable; urgency=medium
+ samtools (1.2-3) unstable; urgency=medium
.
- c448d48 Merge tag '1.1' into debian/unstable
- d12ab1e Merge branch 'develop' into debian/unstable to solve issue
- with regression tests needing a pseudo-terminal.
- See https://github.com/samtools/samtools/issues/300
- c87f8ce Add autopkg tests.
- 7c50b7b Removed python-wrong-path-for-interpreter.patch
- (issue solved upstream).
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
Checksums-Sha1:
- b6e1ad13e7adbb686479035064d939bc6b756735 376830 samtools_1.1-1_kfreebsd-amd64.deb
+ e712b8291a20a1fcfcb86c7275b8a507e2b465ee 394868 samtools_1.2-3_kfreebsd-amd64.deb
Checksums-Sha256:
- 6ce726976ac08ee869cc1814cbc87d52d9efc7b6c2328daadc14e0cbf349cecb 376830 samtools_1.1-1_kfreebsd-amd64.deb
+ c7b3870dbcf43ce2f0b1de042a1f2bf0bb8afd5713d87ccd594b40111a4b62ed 394868 samtools_1.2-3_kfreebsd-amd64.deb
Files:
- d0969c084ef2f415726914fc1baffe1d 376830 science optional samtools_1.1-1_kfreebsd-amd64.deb
+ a4b1bfd85a27ca939e50f4f1d2871499 394868 science optional samtools_1.2-3_kfreebsd-amd64.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
-samtools_1.1-1_kfreebsd-amd64.deb
+samtools_1.2-3_kfreebsd-amd64.deb
─────────────────────────────────
new debian package, version 2.0.
- size 376830 bytes: control archive=1566 bytes.
- 815 bytes, 16 lines control
+ size 394868 bytes: control archive=1496 bytes.
+ 817 bytes, 16 lines control
1557 bytes, 27 lines md5sums
Package: samtools
- Version: 1.1-1
+ Version: 1.2-3
Architecture: kfreebsd-amd64
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1008
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
+ Installed-Size: 1070
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
@@ -1561,41 +1657,41 @@ samtools_1.1-1_kfreebsd-amd64.deb
to retrieve reads in any regions swiftly. It is designed to work on a stream,
and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/bin/
--rwxr-xr-x root/root 767928 2014-09-25 00:31 ./usr/bin/samtools
--rwxr-xr-x root/root 22664 2014-09-25 00:31 ./usr/bin/ace2sam
--rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14440 2014-09-25 00:31 ./usr/bin/md5fa
--rwxr-xr-x root/root 10280 2014-09-25 00:31 ./usr/bin/md5sum-lite
--rwxr-xr-x root/root 22752 2014-09-25 00:31 ./usr/bin/wgsim
--rwxr-xr-x root/root 5328 2014-09-19 15:51 ./usr/bin/blast2sam.pl
--rwxr-xr-x root/root 3364 2014-09-19 15:51 ./usr/bin/bowtie2sam.pl
--rwxr-xr-x root/root 18032 2014-09-19 15:51 ./usr/bin/export2sam.pl
--rwxr-xr-x root/root 6125 2014-09-19 15:51 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 6773 2014-09-19 15:51 ./usr/bin/novo2sam.pl
--rwxr-xr-x root/root 48023 2014-09-19 15:51 ./usr/bin/plot-bamstats
--rwxr-xr-x root/root 3208 2014-09-19 15:51 ./usr/bin/psl2sam.pl
--rwxr-xr-x root/root 8961 2014-09-19 15:51 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 16478 2014-09-19 15:51 ./usr/bin/samtools.pl
--rwxr-xr-x root/root 10789 2014-09-19 15:51 ./usr/bin/seq_cache_populate.pl
--rwxr-xr-x root/root 3909 2014-09-19 15:51 ./usr/bin/soap2sam.pl
--rwxr-xr-x root/root 7888 2014-09-19 15:51 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 4157 2014-09-19 15:51 ./usr/bin/wgsim_eval.pl
--rwxr-xr-x root/root 3583 2014-09-19 15:51 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/man1/
--rw-r--r-- root/root 12774 2014-09-25 00:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/samtools/
--rw-r--r-- root/root 828 2014-09-19 15:51 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2014-09-24 23:56 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2014-09-24 23:56 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3462 2014-09-24 23:56 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 3270 2014-09-25 00:05 ./usr/share/doc/samtools/changelog.Debian.gz
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/bin/
+-rwxr-xr-x root/root 22664 2015-09-22 17:26 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10336 2015-09-22 17:26 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10336 2015-09-22 17:26 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14440 2015-09-22 17:26 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10280 2015-09-22 17:26 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 810616 2015-09-22 17:26 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22752 2015-09-22 17:26 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 17:26 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 17:26 ./usr/share/man/man1/samtools.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -1615,23 +1711,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-amd64
-Build-Space: 15254
-Build-Time: 132
+Build-Space: 15836
+Build-Time: 103
Distribution: sid
Host Architecture: kfreebsd-amd64
-Install-Time: 32
-Job: samtools_1.1-1
+Install-Time: 20
+Job: samtools_1.2-3
Machine Architecture: kfreebsd-amd64
Package: samtools
-Package-Time: 217
-Source-Version: 1.1-1
-Space: 15254
+Package-Time: 178
+Source-Version: 1.2-3
+Space: 15836
Status: successful
-Version: 1.1-1
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0031
-Build needed 00:03:37, 15254k disc space
-Signature with key '8C5D26F3' requested:
- signfile /home/buildd/build/samtools_1.1-1_kfreebsd-amd64.changes 8C5D26F3
+Finished at 20150922-1726
+Build needed 00:02:58, 15836k disc space
+Signature with key '33251A36' requested:
+ signfile /home/buildd/build/samtools_1.2-3_kfreebsd-amd64.changes 33251A36
Successfully signed changes file
diff --git a/kfreebsd-i386.log b/kfreebsd-i386.log
index d9a73f8..67f4b71 100644
--- a/kfreebsd-i386.log
+++ b/kfreebsd-i386.log
@@ -1,73 +1,45 @@
-From buildd at finzi.debian.org Thu Sep 25 00:34:46 2014
-Return-path: <buildd at finzi.debian.org>
-Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at finzi.debian.org>)
- id 1XWx1C-0008E6-Df
- for logs at buildd.debian.org; Thu, 25 Sep 2014 00:34:46 +0000
-Received: from finzi.debian.org ([2607:f8f0:610:4000:6564:a62:19:111])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=finzi.debian.org, EMAIL=hostmaster at finzi.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at finzi.debian.org>)
- id 1XWx1A-0005sy-MD; Thu, 25 Sep 2014 00:34:44 +0000
-Received: from buildd by finzi.debian.org with local (Exim 4.80)
- (envelope-from <buildd at finzi.debian.org>)
- id 1XWx19-000Ash-NH; Thu, 25 Sep 2014 00:34:43 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 00:34:43 +0000
-From: buildd on finzi <buildd at finzi.debian.org>
-To: christoph at debian.org,logs at buildd.debian.org
-Subject: Log for attempted build of samtools_1.1-1 on kfreebsd-i386 (dist=sid)
-Key-Id: A10F7C65
-Message-Id: <E1XWx19-000Ash-NH at finzi.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on finzi.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on fils.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (kfreebsd-i386) 25 Sep 2014 00:24 ║
+║ samtools 1.2-3 (kfreebsd-i386) 22 Sep 2015 18:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
Machine Architecture: kfreebsd-i386
Host Architecture: kfreebsd-i386
Build Architecture: kfreebsd-i386
-I: NOTICE: Log filtering will replace 'build/samtools-qc6QH2/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-qc6QH2' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ki-sbuild-1411604684-24335' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-ZiSBO4/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-ZiSBO4' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-kfreebsd-i386-sbuild-1442945363-90721' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
-Get:2 http://mirror-ubc.debian.org unstable/main Sources [7548 kB]
-Get:3 http://ftp.debian.org unstable InRelease [233 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [57.1 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [107 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-i386 Packages [6486 kB]
-Get:8 http://ftp.debian.org unstable/main Sources [7548 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib kfreebsd-i386 Packages [39.7 kB]
-Get:10 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
-Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
-Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
-Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [291 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [844 B]
-Get:15 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [107 kB]
-Get:17 http://ftp.debian.org unstable/main kfreebsd-i386 Packages [6486 kB]
-Get:18 http://ftp.debian.org unstable/contrib kfreebsd-i386 Packages [39.7 kB]
-Fetched 29.7 MB in 1min 7s (440 kB/s)
+Get:1 http://ftp.de.debian.org unstable InRelease [253 kB]
+Get:2 http://ftp.debian.org unstable InRelease [253 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:5 http://ftp.de.debian.org unstable/main Sources [8093 kB]
+Get:6 http://incoming.debian.org buildd-unstable/main Sources [361 kB]
+Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1252 B]
+Get:9 http://incoming.debian.org buildd-unstable/main kfreebsd-i386 Packages [111 kB]
+Get:10 http://incoming.debian.org buildd-unstable/contrib kfreebsd-i386 Packages [1064 B]
+Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:13 http://ftp.debian.org unstable/main kfreebsd-i386 Packages [6969 kB]
+Get:14 http://ftp.de.debian.org unstable/contrib Sources [59.7 kB]
+Get:15 http://ftp.de.debian.org unstable/non-free Sources [106 kB]
+Get:16 http://ftp.de.debian.org unstable/main kfreebsd-i386 Packages [6969 kB]
+Get:17 http://ftp.debian.org unstable/contrib kfreebsd-i386 Packages [42.6 kB]
+Get:18 http://ftp.de.debian.org unstable/contrib kfreebsd-i386 Packages [42.6 kB]
+Fetched 31.6 MB in 16s (1913 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -88,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 15s (272 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 1s (2697 kB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-VZrg5j/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-eiSkMa/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -115,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 66 not upgraded.
-Need to get 0 B/822 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/776 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10755 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-ZiCUyo/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 10952 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, freebsd-utils, grep, gzip, hostname, init, libc-bin, login, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-Oz6xSm/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -139,185 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
- libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
- zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 25 newly installed, 0 to remove and 63 not upgraded.
-Need to get 10.9 MB/10.9 MB of archives.
-After this operation, 30.3 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin kfreebsd-i386 5.9+20140913-1 [348 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-i386 5.9+20140913-1 [282 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-i386 5.9+20140913-1 [102 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.3.1-1 [27.7 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.2-8 [1073 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.5 [205 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.7.0.1-1 [1002 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-i386 0.19.2-2 [30.8 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.19-2 [242 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.9.1+dfsg1-4 [833 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-i386 3.1-2 [17.3 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.42.0-1 [2539 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.8-3 [140 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-i386 1.1-1 [215 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5.2 [284 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.19-2 [58.1 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.19.2-2 [121 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.19.2-2 [1237 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-i386 1.1-1 [255 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 5.9+20140913-1 [75.9 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 5.9+20140913-1 [176 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-i386 1.1-1 [198 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-2 [205 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 18.3 MB/18.3 MB of archives.
+After this operation, 64.6 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base kfreebsd-i386 1.22.3-1 [1099 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils kfreebsd-i386 9.0.6 [183 kB]
+Get:4 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 kfreebsd-i386 1.4.1-1 [29.8 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main man-db kfreebsd-i386 2.7.3-1 [1006 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libffi6 kfreebsd-i386 3.2.1-3 [18.4 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-i386 2.42.1-1 [2455 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libicu55 kfreebsd-i386 55.1-5 [7761 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 kfreebsd-i386 2.9.2+zdfsg1-4 [920 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libcroco3 kfreebsd-i386 0.6.8-3+b1 [141 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libunistring0 kfreebsd-i386 0.9.3-5.2+b1 [285 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libmagic1 kfreebsd-i386 1:5.25-1 [261 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main file kfreebsd-i386 1:5.25-1 [61.5 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main gettext-base kfreebsd-i386 0.19.6-1 [123 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext kfreebsd-i386 0.19.6-1 [1461 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libhts1 kfreebsd-i386 1.2.1-1 [241 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main libhts-dev kfreebsd-i386 1.2.1-1 [283 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main libio-pty-perl kfreebsd-i386 1:1.08-1+b4 [36.5 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-i386 6.0+20150810-1 [76.4 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-i386 6.0+20150810-1 [173 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main tabix kfreebsd-i386 1.2.1-1 [231 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-i386 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.9 MB in 2s (5416 kB/s)
-(Reading database ... 10755 files and directories currently installed.)
-Preparing to unpack .../ncurses-bin_5.9+20140913-1_kfreebsd-i386.deb ...
-Unpacking ncurses-bin (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up ncurses-bin (5.9+20140913-1) ...
-(Reading database ... 10755 files and directories currently installed.)
-Preparing to unpack .../libtinfo5_5.9+20140913-1_kfreebsd-i386.deb ...
-Unpacking libtinfo5:kfreebsd-i386 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libtinfo5:kfreebsd-i386 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-9) ...
-(Reading database ... 10755 files and directories currently installed.)
-Preparing to unpack .../libncurses5_5.9+20140913-1_kfreebsd-i386.deb ...
-Unpacking libncurses5:kfreebsd-i386 (5.9+20140913-1) over (5.9+20140712-2) ...
-Setting up libncurses5:kfreebsd-i386 (5.9+20140913-1) ...
-Processing triggers for libc-bin (2.19-9) ...
-Selecting previously unselected package libpipeline1:kfreebsd-i386.
-(Reading database ... 10755 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_kfreebsd-i386.deb ...
-Unpacking libpipeline1:kfreebsd-i386 (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_kfreebsd-i386.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5_kfreebsd-i386.deb ...
-Unpacking bsdmainutils (9.0.5) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_kfreebsd-i386.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:kfreebsd-i386.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_kfreebsd-i386.deb ...
-Unpacking libasprintf0c2:kfreebsd-i386 (0.19.2-2) ...
-Selecting previously unselected package libmagic1:kfreebsd-i386.
-Preparing to unpack .../libmagic1_1%3a5.19-2_kfreebsd-i386.deb ...
-Unpacking libmagic1:kfreebsd-i386 (1:5.19-2) ...
-Selecting previously unselected package libxml2:kfreebsd-i386.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4_kfreebsd-i386.deb ...
-Unpacking libxml2:kfreebsd-i386 (2.9.1+dfsg1-4) ...
-Selecting previously unselected package libffi6:kfreebsd-i386.
-Preparing to unpack .../libffi6_3.1-2_kfreebsd-i386.deb ...
-Unpacking libffi6:kfreebsd-i386 (3.1-2) ...
-Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_kfreebsd-i386.deb ...
-Unpacking libglib2.0-0:kfreebsd-i386 (2.42.0-1) ...
-Selecting previously unselected package libcroco3:kfreebsd-i386.
-Preparing to unpack .../libcroco3_0.6.8-3_kfreebsd-i386.deb ...
-Unpacking libcroco3:kfreebsd-i386 (0.6.8-3) ...
-Selecting previously unselected package libhts1:kfreebsd-i386.
-Preparing to unpack .../libhts1_1.1-1_kfreebsd-i386.deb ...
-Unpacking libhts1:kfreebsd-i386 (1.1-1) ...
-Selecting previously unselected package libunistring0:kfreebsd-i386.
-Preparing to unpack .../libunistring0_0.9.3-5.2_kfreebsd-i386.deb ...
-Unpacking libunistring0:kfreebsd-i386 (0.9.3-5.2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_kfreebsd-i386.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_kfreebsd-i386.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_kfreebsd-i386.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:kfreebsd-i386.
-Preparing to unpack .../libhts-dev_1.1-1_kfreebsd-i386.deb ...
-Unpacking libhts-dev:kfreebsd-i386 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_kfreebsd-i386.deb ...
-Unpacking libtinfo-dev:kfreebsd-i386 (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:kfreebsd-i386.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_kfreebsd-i386.deb ...
-Unpacking libncurses5-dev:kfreebsd-i386 (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.1-1_kfreebsd-i386.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:kfreebsd-i386.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_kfreebsd-i386.deb ...
-Unpacking zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:kfreebsd-i386 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:kfreebsd-i386 (0.19.2-2) ...
-Setting up libmagic1:kfreebsd-i386 (1:5.19-2) ...
-Setting up libxml2:kfreebsd-i386 (2.9.1+dfsg1-4) ...
-Setting up libffi6:kfreebsd-i386 (3.1-2) ...
-Setting up libglib2.0-0:kfreebsd-i386 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-i386 (0.6.8-3) ...
-Setting up libhts1:kfreebsd-i386 (1.1-1) ...
-Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:kfreebsd-i386 (1.1-1) ...
-Setting up libtinfo-dev:kfreebsd-i386 (5.9+20140913-1) ...
-Setting up libncurses5-dev:kfreebsd-i386 (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-9) ...
+Fetched 18.3 MB in 2s (8043 kB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 10952 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_kfreebsd-i386.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_kfreebsd-i386.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:kfreebsd-i386.
+Preparing to unpack .../libpipeline1_1.4.1-1_kfreebsd-i386.deb ...
+Unpacking libpipeline1:kfreebsd-i386 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_kfreebsd-i386.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:kfreebsd-i386.
+Preparing to unpack .../libffi6_3.2.1-3_kfreebsd-i386.deb ...
+Unpacking libffi6:kfreebsd-i386 (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:kfreebsd-i386.
+Preparing to unpack .../libglib2.0-0_2.42.1-1_kfreebsd-i386.deb ...
+Unpacking libglib2.0-0:kfreebsd-i386 (2.42.1-1) ...
+Selecting previously unselected package libicu55:kfreebsd-i386.
+Preparing to unpack .../libicu55_55.1-5_kfreebsd-i386.deb ...
+Unpacking libicu55:kfreebsd-i386 (55.1-5) ...
+Selecting previously unselected package libxml2:kfreebsd-i386.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_kfreebsd-i386.deb ...
+Unpacking libxml2:kfreebsd-i386 (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:kfreebsd-i386.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_kfreebsd-i386.deb ...
+Unpacking libcroco3:kfreebsd-i386 (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:kfreebsd-i386.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_kfreebsd-i386.deb ...
+Unpacking libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:kfreebsd-i386.
+Preparing to unpack .../libmagic1_1%3a5.25-1_kfreebsd-i386.deb ...
+Unpacking libmagic1:kfreebsd-i386 (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_kfreebsd-i386.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_kfreebsd-i386.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_kfreebsd-i386.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:kfreebsd-i386.
+Preparing to unpack .../libhts1_1.2.1-1_kfreebsd-i386.deb ...
+Unpacking libhts1:kfreebsd-i386 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:kfreebsd-i386.
+Preparing to unpack .../libhts-dev_1.2.1-1_kfreebsd-i386.deb ...
+Unpacking libhts-dev:kfreebsd-i386 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_kfreebsd-i386.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:kfreebsd-i386.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_kfreebsd-i386.deb ...
+Unpacking libtinfo-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:kfreebsd-i386.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_kfreebsd-i386.deb ...
+Unpacking libncurses5-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_kfreebsd-i386.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:kfreebsd-i386 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:kfreebsd-i386 (3.2.1-3) ...
+Setting up libglib2.0-0:kfreebsd-i386 (2.42.1-1) ...
+No schema files found: doing nothing.
+Setting up libicu55:kfreebsd-i386 (55.1-5) ...
+Setting up libxml2:kfreebsd-i386 (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:kfreebsd-i386 (0.6.8-3+b1) ...
+Setting up libunistring0:kfreebsd-i386 (0.9.3-5.2+b1) ...
+Setting up libmagic1:kfreebsd-i386 (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:kfreebsd-i386 (1.2.1-1) ...
+Setting up libhts-dev:kfreebsd-i386 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Setting up libncurses5-dev:kfreebsd-i386 (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:kfreebsd-i386 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: GNU/kFreeBSD 9.0-2-686 kfreebsd-i386 (i386)
-Toolchain package versions: binutils_2.24.51.20140818-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-8 gcc-4.9_4.9.1-8 kfreebsd-kernel-headers_10.0~5 libc0.1-dev_2.19-9 libstdc++-4.9-dev_4.9.1-8 libstdc++6_4.9.1-8
-Package versions: apt_1.0.6 base-files_7.5 base-passwd_3.5.33 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140818-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.21-1.2 cpp_4:4.9.1-3 cpp-4.9_4.9.1-8 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2012.4 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.11-2 e2fsprogs_1.42.11-2 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_ [...]
+Kernel: GNU/kFreeBSD 10.1-0-686 kfreebsd-i386 (i386)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 kfreebsd-kernel-headers_10.1~5 libc0.1-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17
+Package versions: apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-1 findutils_4.4 [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -328,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -352,11 +322,11 @@ HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=sid-kfreebsd-i386-sbuild
-SCHROOT_CHROOT_NAME=sid-ki-sbuild
+SCHROOT_CHROOT_NAME=sid-kfreebsd-i386-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ki-sbuild-1411604684-24335
+SCHROOT_SESSION_ID=sid-kfreebsd-i386-sbuild-1442945363-90721
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -366,11 +336,11 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture kfreebsd-i386
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
@@ -390,9 +360,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -429,8 +401,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -439,10 +410,6 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
-padding.c: In function 'bam_pad2unpad':
-padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
- fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
@@ -461,10 +428,6 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
-misc/ace2sam.c: In function 'main':
-misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
- fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
@@ -475,15 +438,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
-test/merge/test_rtrans_build.c: In function 'main':
-test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMIC_SEED = 0x1234abcd330e;
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
-test/merge/test_trans_tbl_init.c: In function 'main':
-test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMMICK_SEED = 0x1234abcd330e;
- ^
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
@@ -491,6 +446,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
@@ -506,7 +462,7 @@ gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/tes
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lcurs [...]
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/i386-kfreebsd-gnu/libhts.a -lhts -lcurses -lm -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -518,248 +474,262 @@ dh_auto_test -- \
make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/pJK7mljtU5/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/ffJ8jRQaFI/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/pJK7mljtU5/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/ffJ8jRQaFI/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/pJK7mljtU5/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/ffJ8jRQaFI/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/pJK7mljtU5/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/ffJ8jRQaFI/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/pJK7mljtU5/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/ffJ8jRQaFI/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/pJK7mljtU5/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/ffJ8jRQaFI/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/pJK7mljtU5/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/ffJ8jRQaFI/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/pJK7mljtU5/mpileup.bam.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/ffJ8jRQaFI/mpileup.bam.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pJK7mljtU5/mpileup.bam.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ffJ8jRQaFI/mpileup.bam.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/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/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/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/pJK7mljtU5/mpileup.cram.list -f /tmp/pJK7mljtU5/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/ffJ8jRQaFI/mpileup.cram.list -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pJK7mljtU5/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ffJ8jRQaFI/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/pJK7mljtU5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/pJK7mljtU5/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ffJ8jRQaFI/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ffJ8jRQaFI/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
-test_view:
- Generating test data file .................. done
- 1: SAM -> BAM -> SAM
- SAM files differ at /tmp/pJK7mljtU5/view.test001.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test001.bam -b /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test001.bam.sam /tmp/pJK7mljtU5/view.test001.bam
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+test_usage_subcommand:
+ samtools faidx
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 2: SAM -> uncompressed BAM .. ok
+test_usage_subcommand:
+ samtools index
+.. ok
- 3: uncompressed BAM -> SAM and compare
- SAM files differ at /tmp/pJK7mljtU5/view.test003.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test003.sam -h /tmp/pJK7mljtU5/view.test002.bam
+test_usage_subcommand:
+ samtools calmd
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools fixmate
+.. ok
- 4: SAM -> fast compressed BAM .. ok
+test_usage_subcommand:
+ samtools reheader
- 5: fast compressed BAM -> SAM and compare
- SAM files differ at /tmp/pJK7mljtU5/view.test005.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test005.sam -h /tmp/pJK7mljtU5/view.test004.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools rmdup
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 6: SAM -> CRAM -> SAM (UR header tags)
- SAM files differ at /tmp/pJK7mljtU5/view.test006.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test006.cram -C /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test006.cram.sam /tmp/pJK7mljtU5/view.test006.cram
+test_usage_subcommand:
+ samtools targetcut
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools bamshuf
- 7: SAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/pJK7mljtU5/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test007.cram.sam /tmp/pJK7mljtU5/view.test007.cram
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools cat
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 8: BAM -> CRAM with UR -> SAM
- SAM files differ at /tmp/pJK7mljtU5/view.test008.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test008.cram -C /tmp/pJK7mljtU5/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test008.cram.sam /tmp/pJK7mljtU5/view.test008.cram
+test_usage_subcommand:
+ samtools merge
+.. ok
+test_usage_subcommand:
+ samtools mpileup
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 9: SAM -> BAM (M5 header tags)
- SAM files differ at /tmp/pJK7mljtU5/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test009.bam.sam /tmp/pJK7mljtU5/view.test009.bam
+test_usage_subcommand:
+ samtools sort
+.. ok
+test_usage_subcommand:
+ samtools split
+.. ok
-.. failed ...
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
- 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/pJK7mljtU5/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test010.cram -C /tmp/pJK7mljtU5/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test010.cram.sam /tmp/pJK7mljtU5/view.test010.cram
+test_usage_subcommand:
+ samtools bedcov
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools depth
- 11: CRAM -> BAM with UR
- SAM files differ at /tmp/pJK7mljtU5/view.test011.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test011.bam -b /tmp/pJK7mljtU5/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test011.bam.sam /tmp/pJK7mljtU5/view.test011.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools flagstat
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 12: CRAM -> BAM with M5
- SAM files differ at /tmp/pJK7mljtU5/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test012.bam -b /tmp/pJK7mljtU5/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test012.bam.sam /tmp/pJK7mljtU5/view.test012.bam
+test_usage_subcommand:
+ samtools idxstats
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools phase
- 13: SAM -> SAM via stdout
- SAM files differ at /tmp/pJK7mljtU5/view.test013.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/view.001.sam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools stats
+.. ok
-.. failed ...
+test_usage_subcommand:
+ samtools flags
- 14: SAM -> BAM via stdout .. ok
+ Usage on stderr rather than stdout
+.. expected failure
- 15: SAM -> CRAM via stdout
- SAM files differ at /tmp/pJK7mljtU5/view.test015.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -C /tmp/pJK7mljtU5/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test015.cram.sam /tmp/pJK7mljtU5/view.test015.cram
+test_usage_subcommand:
+ samtools tview
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools view
- 16: SAM from stdin -> SAM
- SAM files differ at /tmp/pJK7mljtU5/view.test016.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test016.sam -h -
+ Usage on stderr rather than stdout
+.. expected failure
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
-.. failed ...
+ 2: SAM -> uncompressed BAM .. ok
- 17: BAM from stdin -> SAM
- SAM files differ at /tmp/pJK7mljtU5/view.test017.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test017.sam -h -
+ 3: uncompressed BAM -> SAM and compare .. ok
+ 4: SAM -> fast compressed BAM .. ok
-.. failed ...
+ 5: fast compressed BAM -> SAM and compare .. ok
- 18: CRAM from stdin -> SAM
- SAM files differ at /tmp/pJK7mljtU5/view.test018.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test018.sam -h -
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
-.. failed ...
+ 8: BAM -> CRAM with UR -> SAM .. ok
- 19: samtools view -H (SAM input) .. ok
+ 9: SAM -> BAM (M5 header tags) .. ok
- 20: samtools view -H (BAM input) .. ok
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
- 21: samtools view -H (CRAM input) .. ok
+ 11: CRAM -> BAM with UR .. ok
+
+ 12: CRAM -> BAM with M5 .. ok
- 22: No headers (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test022.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test022.body /tmp/pJK7mljtU5/view.001.sam
+ 13: SAM -> SAM via stdout .. ok
+
+ 14: SAM -> BAM via stdout .. ok
+ 15: SAM -> CRAM via stdout .. ok
-.. failed ...
+ 16: SAM from stdin -> SAM .. ok
- 23: No headers (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test023.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test023.body /tmp/pJK7mljtU5/view.test001.bam
+ 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
-.. failed ...
+ 21: samtools view -H (CRAM input) .. ok
- 24: No headers (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test024.body : 6 / /tmp/pJK7mljtU5/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test024.body /tmp/pJK7mljtU5/view.test006.cram
+ 22: No headers (SAM input) .. ok
+ 23: No headers (BAM input) .. ok
-.. failed ...
+ 24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
@@ -773,206 +743,116 @@ test_view:
30: Count -f 128 (CRAM input) .. ok
- 31: Filter -F 128 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test031.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test031.sam -h -F 128 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
- 33: Filter -F 128 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test033.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test033.sam -h -F 128 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
- 35: Filter -F 128 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test035.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test035.sam -h -F 128 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
- 37: Filter -F 128 -f 2 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test037.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test037.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/pJK7mljtU5/view.test039.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test039.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/pJK7mljtU5/view.test041.sam : 34 / /tmp/pJK7mljtU5/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test041.sam -h -F 128 -f 2 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
- 43: Filter -r grp2 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test043.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test043.sam -h -r grp2 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
- 45: Filter -r grp2 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test045.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test045.sam -h -r grp2 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
- 47: Filter -r grp2 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test047.sam : 29 / /tmp/pJK7mljtU5/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test047.sam -h -r grp2 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/pJK7mljtU5/view.001.fogn (SAM input) .. ok
-
- 50: Count -R /tmp/pJK7mljtU5/view.001.fogn (SAM input) .. ok
-
- 51: Filter -R /tmp/pJK7mljtU5/view.001.fogn (BAM input) .. ok
+ 49: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input) .. ok
- 52: Count -R /tmp/pJK7mljtU5/view.001.fogn (BAM input) .. ok
+ 50: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input) .. ok
- 53: Filter -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input) .. ok
+ 51: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input) .. ok
- 54: Count -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input) .. ok
+ 52: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input) .. ok
- 55: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test055.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test055.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.001.sam
+ 53: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input) .. ok
-.. failed ...
+ 55: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test057.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test057.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.test001.bam
+ 57: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (BAM input).. ok
-.. failed ...
+ 59: Filter -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (CRAM input).. ok
- 58: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (BAM input).. ok
+ 60: Count -R /tmp/ffJ8jRQaFI/view.001.fogn -r grp2 (CRAM input).. ok
- 59: Filter -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test059.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test059.sam -h -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 /tmp/pJK7mljtU5/view.test006.cram
+ 61: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (SAM input).. ok
-.. failed ...
+ 63: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input).. ok
- 60: Count -R /tmp/pJK7mljtU5/view.001.fogn -r grp2 (CRAM input).. ok
+ 64: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (BAM input).. ok
- 61: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test061.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test061.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.001.sam
+ 65: Filter -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input).. ok
-
-.. failed ...
-
- 62: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (SAM input).. ok
-
- 63: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test063.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test063.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
-
- 64: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (BAM input).. ok
-
- 65: Filter -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test065.sam : 34 / /tmp/pJK7mljtU5/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test065.sam -h -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
-
- 66: Count -r grp2 -R /tmp/pJK7mljtU5/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/ffJ8jRQaFI/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test067.sam -h -l Library 2 /tmp/pJK7mljtU5/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/ffJ8jRQaFI/view.test067.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ffJ8jRQaFI/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test069.sam -h -l Library 2 /tmp/pJK7mljtU5/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/ffJ8jRQaFI/view.test069.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ffJ8jRQaFI/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test071.sam -h -l Library 2 /tmp/pJK7mljtU5/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/ffJ8jRQaFI/view.test071.sam -h -l Library 2 /tmp/ffJ8jRQaFI/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/pJK7mljtU5/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ffJ8jRQaFI/view.test006.cram
.. expected failure
@@ -1013,153 +893,63 @@ Samtools-htslib-API: bam_get_library() not yet implemented
90: Count -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test091.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test091.sam -h -x fa /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 91: Filter -x fa (SAM input) .. ok
92: Count -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test093.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test093.sam -h -x fa /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 93: Filter -x fa (BAM input) .. ok
94: Count -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test095.sam : 34 / /tmp/pJK7mljtU5/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test095.sam -h -x fa /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 95: Filter -x fa (CRAM input) .. ok
96: Count -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test097.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test097.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 97: Filter -x fa -x ha (SAM input) .. ok
98: Count -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test099.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test099.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 99: Filter -x fa -x ha (BAM input) .. ok
100: Count -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test101.sam : 34 / /tmp/pJK7mljtU5/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test101.sam -h -x fa -x ha /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 101: Filter -x fa -x ha (CRAM input) .. ok
102: Count -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test103.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test103.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
104: Count -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test105.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test105.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
106: Count -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test107.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test107.sam -h -x fa -r grp2 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
108: Count -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test109.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test109.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
110: Count -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test111.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test111.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
112: Count -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test113.sam : 29 / /tmp/pJK7mljtU5/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test113.sam -h -x RG -r grp2 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
114: Count -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test115.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test115.sam -h -m 10 /tmp/pJK7mljtU5/view.001.sam
-
-
-.. failed ...
+ 115: Filter -m 10 (SAM input) .. ok
116: Count -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test117.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test117.sam -h -m 10 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 117: Filter -m 10 (BAM input) .. ok
118: Count -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test119.sam : 34 / /tmp/pJK7mljtU5/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test119.sam -h -m 10 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 119: Filter -m 10 (CRAM input) .. ok
120: Count -m 10 (CRAM input) .. ok
@@ -1227,143 +1017,59 @@ Samtools-htslib-API: bam_get_library() not yet implemented
151: Count Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test152.sam : 34 / /tmp/pJK7mljtU5/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test152.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1
-
-
-.. failed ...
+ 152: Region ref1 (BAM input) .. ok
153: Count ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test154.sam : 34 / /tmp/pJK7mljtU5/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test154.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1
-
-
-.. failed ...
+ 154: Region ref1 (CRAM input) .. ok
155: Count ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test156.sam : 31 / /tmp/pJK7mljtU5/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test156.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15
-
-
-.. failed ...
+ 156: Region ref1:15 (BAM input) .. ok
157: Count ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test158.sam : 31 / /tmp/pJK7mljtU5/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test158.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15
-
-
-.. failed ...
+ 158: Region ref1:15 (CRAM input) .. ok
159: Count ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test160.sam : 31 / /tmp/pJK7mljtU5/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test160.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 160: Region ref1:15-45 (BAM input) .. ok
161: Count ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test162.sam : 31 / /tmp/pJK7mljtU5/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test162.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 162: Region ref1:15-45 (CRAM input) .. ok
163: Count ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test164.sam : 31 / /tmp/pJK7mljtU5/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test164.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2
-
-
-.. failed ...
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
165: Count ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test166.sam : 31 / /tmp/pJK7mljtU5/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test166.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2
-
-
-.. failed ...
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
167: Count ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test168.sam : 31 / /tmp/pJK7mljtU5/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test168.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2:16
-
-
-.. failed ...
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
169: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test170.sam : 31 / /tmp/pJK7mljtU5/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test170.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2:16
-
-
-.. failed ...
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test172.sam : 31 / /tmp/pJK7mljtU5/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test172.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test174.sam : 31 / /tmp/pJK7mljtU5/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test174.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test176.sam : 31 / /tmp/pJK7mljtU5/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test176.sam -h /tmp/pJK7mljtU5/view.test001.bam ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test178.sam : 31 / /tmp/pJK7mljtU5/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test178.sam -h /tmp/pJK7mljtU5/view.test006.cram ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
@@ -1383,23 +1089,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
187: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test188.sam : 28 / /tmp/pJK7mljtU5/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test188.sam -h -r grp2 /tmp/pJK7mljtU5/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
189: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test190.sam : 28 / /tmp/pJK7mljtU5/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test190.sam -h -r grp2 /tmp/pJK7mljtU5/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
@@ -1419,43 +1113,19 @@ Samtools-htslib-API: bam_get_library() not yet implemented
199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test200.sam : 33 / /tmp/pJK7mljtU5/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 200: 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
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test202.sam : 33 / /tmp/pJK7mljtU5/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 202: 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
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test204.sam : 34 / /tmp/pJK7mljtU5/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 204: 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
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test206.sam : 34 / /tmp/pJK7mljtU5/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 206: 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
@@ -1491,23 +1161,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
223: 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)
- SAM files differ at /tmp/pJK7mljtU5/view.test224.sam : 33 / /tmp/pJK7mljtU5/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test001.bam ref1:11-16
-
-
-.. failed ...
+ 224: 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
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test226.sam : 33 / /tmp/pJK7mljtU5/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/pJK7mljtU5/view.test006.cram ref1:11-16
-
-
-.. failed ...
+ 226: 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
@@ -1535,23 +1193,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
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 -q 5 (BAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test240.sam : 29 / /tmp/pJK7mljtU5/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/pJK7mljtU5/view.test001.bam
-
-
-.. failed ...
+ 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 -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
- SAM files differ at /tmp/pJK7mljtU5/view.test242.sam : 29 / /tmp/pJK7mljtU5/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/pJK7mljtU5/view.test006.cram
-
-
-.. failed ...
+ 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 -q 5 (CRAM input).. ok
@@ -1563,141 +1209,67 @@ Samtools-htslib-API: bam_get_library() not yet implemented
247: 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
- SAM files differ at /tmp/pJK7mljtU5/view.001.no_sq.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.001.no_sq.bam -b /tmp/pJK7mljtU5/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.001.no_sq.bam.sam /tmp/pJK7mljtU5/view.001.no_sq.bam
-
-
-.. failed ...
-
- 249: Add @SQ with -t (SAM -> SAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test249.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam
-
-
-.. failed ...
-
- 250: Add @SQ with -T (SAM -> SAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test250.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam
-
-
-.. failed ...
-
- 251: Add @SQ with -t (BAM -> SAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test251.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam
-
-
-.. failed ...
+ 248: Make BAM with no M5/UR tags .. ok
- 252: Add @SQ with -T (BAM -> SAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test252.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
-.. failed ...
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test253.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test253.bam.sam /tmp/pJK7mljtU5/view.test253.bam
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
-.. failed ...
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test254.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test254.bam.sam /tmp/pJK7mljtU5/view.test254.bam
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
-.. failed ...
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test255.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test255.bam.sam /tmp/pJK7mljtU5/view.test255.bam
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
-.. failed ...
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test256.bam.sam : 34 / /tmp/pJK7mljtU5/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test256.bam.sam /tmp/pJK7mljtU5/view.test256.bam
+ 261: Make CRAM with no UR field .. ok
+ 262: Decoding CRAM with no UR field via -T .. ok
-.. failed ...
+ 263: CIGAR B-operator removal .. ok
- 257: Add @SQ with -t (SAM -> CRAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test257.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test257.cram.sam /tmp/pJK7mljtU5/view.test257.cram
+ 264: Big SAM -> BAM .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
-.. failed ...
+ 266: Big SAM -> BAM (4 threads) .. ok
- 258: Add @SQ with -T (SAM -> CRAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test258.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test258.cram.sam /tmp/pJK7mljtU5/view.test258.cram
+ 267: Big SAM -> CRAM .. ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
-.. failed ...
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 259: Add @SQ with -t (BAM -> CRAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test259.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test259.cram.sam /tmp/pJK7mljtU5/view.test259.cram
+ 270: Subsample 0.2 (SAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
-.. failed ...
+ 272: Subsample 0.8 (SAM input) ............ ok
- 260: Add @SQ with -T (BAM -> CRAM)
- SAM files differ at /tmp/pJK7mljtU5/view.test260.cram.sam : 34 / /tmp/pJK7mljtU5/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/pJK7mljtU5/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/pJK7mljtU5/view.test260.cram.sam /tmp/pJK7mljtU5/view.test260.cram
+ 273: Subsample 0.2 (BAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
-.. failed ...
+ 275: Subsample 0.8 (BAM input) ............ ok
- 261: CIGAR B-operator removal .. ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
- 262: Big SAM -> BAM .. ok
+ 277: Subsample 0.5 (CRAM input) ............ ok
- 263: Big SAM -> BAM (2 threads) .. ok
-
- 264: Big SAM -> BAM (4 threads) .. ok
-
- 265: Big SAM -> CRAM .. ok
-
- 266: Big SAM -> CRAM (2 threads) .. ok
-
- 267: Big SAM -> CRAM (4 threads) .. ok
-
- 268: Subsample 0.2 (SAM input) ............ ok
-
- 269: Subsample 0.5 (SAM input) ............ ok
-
- 270: Subsample 0.8 (SAM input) ............ ok
-
- 271: Subsample 0.2 (BAM input) ............ ok
-
- 272: Subsample 0.5 (BAM input) ............ ok
-
- 273: Subsample 0.8 (BAM input) ............ ok
-
- 274: Subsample 0.2 (CRAM input) ............ ok
-
- 275: Subsample 0.5 (CRAM input) ............ ok
-
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1725,21 +1297,10 @@ test_cat:
6: cat recompressed BAM files with new header .. ok
test_bam2fq:
- Generate BAM file
- SAM files differ at GLOB(0x84f07d8) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/bam2fq.001.bam
-
-
-.. failed ...
-
- Generate CRAM file
- SAM files differ at GLOB(0x85ff1a8) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/pJK7mljtU5/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/pJK7mljtU5/bam2fq.001.cram
-
+ Generate BAM file .. ok
-.. failed ...
+Unsorted mode enabled
+ Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
1: bam2fq (SAM input) .. ok
@@ -1792,28 +1353,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/pJK7mljtU5/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/ffJ8jRQaFI/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/pJK7mljtU5/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/ffJ8jRQaFI/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/pJK7mljtU5/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/ffJ8jRQaFI/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/pJK7mljtU5/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/ffJ8jRQaFI/depad.001p.bam
.. expected failure
@@ -1844,16 +1405,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 41286 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/DcqMtJB7dl
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/V7O4LqEkef - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/0JNqdc92H7 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1887,29 +1446,257 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 237
- failed .. 87
- expected failure .. 18
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
unexpected pass .. 0
-Makefile:183: recipe for target 'test' failed
-make[2]: *** [test] Error 1
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
make[2]: Leaving directory '/«PKGBUILDDIR»'
-dh_auto_test: make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
-debian/rules:18: 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 \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a
+ install -d debian/samtools
+ make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/i386-kfreebsd-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/i386-kfreebsd-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_kfreebsd-i386.deb'.
+ dpkg-genchanges -B -mkfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org> >../samtools_1.2-3_kfreebsd-i386.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0034
+Build finished at 20150922-1812
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_kfreebsd-i386.changes:
+─────────────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: kfreebsd-i386
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: kfreebsd-i386 Build Daemon (fils) <buildd_kfreebsd-i386-fils at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ 47eba0a0ca450914e59152b0e9c7adac88237fbe 408396 samtools_1.2-3_kfreebsd-i386.deb
+Checksums-Sha256:
+ bd3e2c723b73aa8925ee16069eee7bc5f6668405bd4b82991f6478c718525487 408396 samtools_1.2-3_kfreebsd-i386.deb
+Files:
+ 7cc5518b37c2b69965bd8222a604140a 408396 science optional samtools_1.2-3_kfreebsd-i386.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_kfreebsd-i386.deb
+────────────────────────────────
+
+ new debian package, version 2.0.
+ size 408396 bytes: control archive=1496 bytes.
+ 816 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: kfreebsd-i386
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1111
+ Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/bin/
+-rwxr-xr-x root/root 17812 2015-09-22 18:11 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9600 2015-09-22 18:11 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9600 2015-09-22 18:11 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13696 2015-09-22 18:11 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9572 2015-09-22 18:11 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 866564 2015-09-22 18:11 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 17872 2015-09-22 18:11 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 18:11 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 18:11 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1923,20 +1710,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: kfreebsd-i386
-Build-Space: 20484
-Build-Time: 297
+Build-Space: 15540
+Build-Time: 103
Distribution: sid
-Fail-Stage: build
Host Architecture: kfreebsd-i386
-Install-Time: 112
-Job: samtools_1.1-1
+Install-Time: 16
+Job: samtools_1.2-3
Machine Architecture: kfreebsd-i386
Package: samtools
-Package-Time: 586
-Source-Version: 1.1-1
-Space: 20484
-Status: attempted
-Version: 1.1-1
+Package-Time: 160
+Source-Version: 1.2-3
+Space: 15540
+Status: successful
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0034
-Build needed 00:09:46, 20484k disc space
+Finished at 20150922-1812
+Build needed 00:02:40, 15540k disc space
+Signature with key 'E3D16566' requested:
+ signfile /home/buildd/build/samtools_1.2-3_kfreebsd-i386.changes E3D16566
+
+Successfully signed changes file
diff --git a/mips.log b/mips.log
deleted file mode 100644
index dc278ca..0000000
--- a/mips.log
+++ /dev/null
@@ -1,1830 +0,0 @@
-From buildd at lucatelli.debian.org Sat Mar 30 14:22:50 2013
-Return-path: <buildd at lucatelli.debian.org>
-Received: from mailly.debian.org ([82.195.75.114])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at lucatelli.debian.org>)
- id 1ULwgE-0006uV-58
- for logs at buildd.debian.org; Sat, 30 Mar 2013 14:22:50 +0000
-Received: from lucatelli.debian.org ([206.12.19.15])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lucatelli.debian.org,
- EMAIL=hostmaster at lucatelli.debian.org (verified)
- by mailly.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at lucatelli.debian.org>)
- id 1ULwgC-00049P-JK
- for logs at buildd.debian.org; Sat, 30 Mar 2013 14:22:49 +0000
-Received: from buildd by lucatelli.debian.org with local (Exim 4.72)
- (envelope-from <buildd at lucatelli.debian.org>) id 1ULwYe-0006xs-4T
- for logs at buildd.debian.org; Sat, 30 Mar 2013 14:15:00 +0000
-Date: Sat, 30 Mar 2013 14:15:00 +0000
-Message-Id: <E1ULwYe-0006xs-4T at lucatelli.debian.org>
-From: buildd on lucatelli <buildd at lucatelli.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on mips (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lucatelli.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (mips) 30 Mar 2013 13:47 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: mips
-Get:1 http://mirror-ubc.debian.org unstable Release.gpg [836 B]
-Get:2 http://mirror-ubc.debian.org unstable Release [235 kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:4 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:5 http://mirror-ubc.debian.org unstable/main Sources [6484 kB]
-Get:6 http://incoming.debian.org unstable Release [235 kB]
-Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:9 http://mirror-ubc.debian.org unstable/contrib Sources [51.0 kB]
-Get:10 http://mirror-ubc.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://mirror-ubc.debian.org unstable/main mips Packages [6073 kB]
-Get:12 http://mirror-ubc.debian.org unstable/contrib mips Packages [36.1 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main mips Packages [6073 kB]
-Get:16 http://incoming.debian.org unstable/contrib mips Packages [36.1 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [18.3 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main mips Packages [13.4 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib mips Packages [14 B]
-Fetched 26.1 MB in 1min 43s (252 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (404 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 6 not upgraded.
-Need to get 9994 kB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 mips 1.2.2-2 [37.2 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main groff-base mips 1.22.2-1 [708 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils mips 9.0.4 [209 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main man-db mips 2.6.3-3 [867 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 mips 0.18.1.1-10 [27.1 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 mips 1:5.11-2.1 [201 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main libpcre3 mips 1:8.31-2 [250 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 mips 2.8.0+dfsg1-7+nmu1 [870 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libffi5 mips 3.0.10-3 [23.0 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 mips 2.33.12+really2.32.4-5 [1686 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 mips 0.6.6-2 [118 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 mips 0.9.3-5 [411 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo0 mips 0.18.1.1-10 [140 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main file mips 1:5.11-2.1 [51.6 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base mips 0.18.1.1-10 [141 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main html2text mips 1.3.2a-15 [103 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf-dev mips 0.18.1.1-10 [26.9 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main libgettextpo-dev mips 0.18.1.1-10 [189 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main gettext mips 0.18.1.1-10 [1753 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main diffstat mips 1.55-3 [28.7 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev mips 5.9-10 [104 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev mips 5.9-10 [223 kB]
-Get:28 http://mirror-ubc.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev mips 1:1.2.7.dfsg-13 [213 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9994 kB in 10s (995 kB/s)
-Selecting previously unselected package libpipeline1:mips.
-(Reading database ... 10799 files and directories currently installed.)
-Unpacking libpipeline1:mips (from .../libpipeline1_1.2.2-2_mips.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_mips.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mips.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_mips.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:mips.
-Unpacking libasprintf0c2:mips (from .../libasprintf0c2_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package libmagic1:mips.
-Unpacking libmagic1:mips (from .../libmagic1_1%3a5.11-2.1_mips.deb) ...
-Selecting previously unselected package libpcre3:mips.
-Unpacking libpcre3:mips (from .../libpcre3_1%3a8.31-2_mips.deb) ...
-Selecting previously unselected package libxml2:mips.
-Unpacking libxml2:mips (from .../libxml2_2.8.0+dfsg1-7+nmu1_mips.deb) ...
-Selecting previously unselected package libffi5:mips.
-Unpacking libffi5:mips (from .../libffi5_3.0.10-3_mips.deb) ...
-Selecting previously unselected package libglib2.0-0:mips.
-Unpacking libglib2.0-0:mips (from .../libglib2.0-0_2.33.12+really2.32.4-5_mips.deb) ...
-Selecting previously unselected package libcroco3:mips.
-Unpacking libcroco3:mips (from .../libcroco3_0.6.6-2_mips.deb) ...
-Selecting previously unselected package libunistring0:mips.
-Unpacking libunistring0:mips (from .../libunistring0_0.9.3-5_mips.deb) ...
-Selecting previously unselected package libgettextpo0:mips.
-Unpacking libgettextpo0:mips (from .../libgettextpo0_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_mips.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mips.deb) ...
-Selecting previously unselected package libasprintf-dev:mips.
-Unpacking libasprintf-dev:mips (from .../libasprintf-dev_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package libgettextpo-dev:mips.
-Unpacking libgettextpo-dev:mips (from .../libgettextpo-dev_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_mips.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_mips.deb) ...
-Selecting previously unselected package libtinfo-dev:mips.
-Unpacking libtinfo-dev:mips (from .../libtinfo-dev_5.9-10_mips.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mips.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:mips.
-Unpacking zlib1g-dev:mips (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mips.deb) ...
-Setting up libpipeline1:mips (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:mips (0.18.1.1-10) ...
-Setting up libmagic1:mips (1:5.11-2.1) ...
-Setting up libpcre3:mips (1:8.31-2) ...
-Setting up libxml2:mips (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:mips (3.0.10-3) ...
-Setting up libglib2.0-0:mips (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:mips (0.6.6-2) ...
-Setting up libunistring0:mips (0.9.3-5) ...
-Setting up libgettextpo0:mips (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:mips (0.18.1.1-10) ...
-Setting up libgettextpo-dev:mips (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:mips (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:mips (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 3.2.0-0.bpo.4-octeon mips (mips64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture mips
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mips-5n0bWE/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mips.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mips.deb'.
- dpkg-genchanges -B -mmips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org> >../samtools_0.1.19-1_mips.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-1414
-
-samtools_0.1.19-1_mips.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: mips
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: mips Build Daemon (lucatelli) <buildd_mips-lucatelli at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 25756739b5ab40f2bdf4a9e66464948459c07689 552640 samtools_0.1.19-1_mips.deb
- f3b538a87375e06336c19afa8374732f072312fb 129524 libbam-dev_0.1.19-1_mips.deb
-Checksums-Sha256:
- d174a100849d8d5b42662b084beb54e3f990fc9e822f604c20ff2acf3a32bb06 552640 samtools_0.1.19-1_mips.deb
- 0a4ec06874f80151a9fa41ef9962e94eb399028786b7386e05105a73cd568fb7 129524 libbam-dev_0.1.19-1_mips.deb
-Files:
- d26e2e39fbd0fa15e5d42808aa721dd1 552640 science optional samtools_0.1.19-1_mips.deb
- 4a5151e4f29a9ad33fde3b1b59a2457a 129524 libdevel optional libbam-dev_0.1.19-1_mips.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_mips.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 552640 bytes: control archive= 1935 bytes.
- 32 bytes, 1 lines conffiles
- 791 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1439
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 14:13 ./
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/samtools/
--rwxr-xr-x root/root 18192 2013-03-30 14:13 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 10032 2013-03-30 14:13 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10068 2013-03-30 14:13 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 14224 2013-03-30 14:13 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10032 2013-03-30 14:13 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 207416 2013-03-30 14:13 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 18508 2013-03-30 14:13 ./usr/lib/samtools/wgsim
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/bin/
--rwxr-xr-x root/root 176252 2013-03-30 14:13 ./usr/bin/bcftools
--rwxr-xr-x root/root 483460 2013-03-30 14:13 ./usr/bin/samtools
--rwxr-xr-x root/root 31780 2013-03-30 14:13 ./usr/bin/razip
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 14:13 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/samtools/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126580 2013-03-30 14:00 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 1966 2013-03-30 14:13 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 14:13 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 14:13 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 14:13 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_mips.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 129524 bytes: control archive= 928 bytes.
- 711 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: mips
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 441
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/lib/
--rw-r--r-- root/root 328998 2013-03-30 14:13 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/include/samtools/
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 14:13 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mips-sbuild-d7aeb6e0-a385-42f3-8e4b-724cf54e9acc/build/buildd-samtools_0.1.19-1-mips-5n0bWE
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: mips
-Build-Space: 12848
-Build-Time: 1396
-Distribution: sid
-Install-Time: 108
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 1660
-Source-Version: 0.1.19-1
-Space: 12848
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-1414
-Build needed 00:27:40, 12848k disc space
-Signature with key 'A2DB4074' requested:
-
-From buildd at mayer.debian.org Sat Mar 30 09:25:04 2013
-Return-path: <buildd at mayer.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at mayer.debian.org>)
- id 1ULs22-0003vN-UH
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:03 +0000
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- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at mayer.debian.org>)
- id 1ULs1z-0007jf-Uy
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:25:00 +0000
-Received: from buildd by mayer.debian.org with local (Exim 4.72)
- (envelope-from <buildd at mayer.debian.org>) id 1ULs1x-0005a0-Te
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:24:58 +0000
-Date: Sat, 30 Mar 2013 09:24:57 +0000
-Message-Id: <E1ULs1x-0005a0-Te at mayer.debian.org>
-From: buildd on mayer <buildd at mayer.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on mipsel (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on mayer.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (mipsel) 30 Mar 2013 09:16 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: mipsel
-Hit http://debian.oregonstate.edu sid Release.gpg
-Hit http://debian.oregonstate.edu sid Release
-Get:1 http://incoming.debian.org sid Release.gpg [836 B]
-Get:2 http://incoming.debian.org Release.gpg [836 B]
-Hit http://debian.oregonstate.edu sid/main Sources
-Hit http://debian.oregonstate.edu sid/contrib Sources
-Hit http://debian.oregonstate.edu sid/main mipsel Packages
-Get:3 http://incoming.debian.org sid Release [235 kB]
-Hit http://debian.oregonstate.edu sid/contrib mipsel Packages
-Get:4 http://incoming.debian.org Release [1141 B]
-Get:5 http://incoming.debian.org sid/main Sources [6484 kB]
-Get:6 http://incoming.debian.org sid/contrib Sources [51.0 kB]
-Get:7 http://incoming.debian.org sid/main mipsel Packages [6075 kB]
-Get:8 http://incoming.debian.org sid/contrib mipsel Packages [36.1 kB]
-Get:9 http://incoming.debian.org Sources [12.5 kB]
-Get:10 http://incoming.debian.org Packages [98.1 kB]
-Fetched 13.0 MB in 38s (334 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/buildd-unstable/ samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (449 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
-Need to get 193 kB/9997 kB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://debian.oregonstate.edu/debian/ sid/main bash-completion all 1:2.0-1 [193 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 193 kB in 0s (2393 kB/s)
-Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10900 files and directories currently installed.)
-Unpacking libpipeline1:mipsel (from .../libpipeline1_1.2.2-2_mipsel.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_mipsel.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_mipsel.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_mipsel.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:mipsel.
-Unpacking libasprintf0c2:mipsel (from .../libasprintf0c2_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package libmagic1:mipsel.
-Unpacking libmagic1:mipsel (from .../libmagic1_1%3a5.11-2.1_mipsel.deb) ...
-Selecting previously unselected package libpcre3:mipsel.
-Unpacking libpcre3:mipsel (from .../libpcre3_1%3a8.31-2_mipsel.deb) ...
-Selecting previously unselected package libxml2:mipsel.
-Unpacking libxml2:mipsel (from .../libxml2_2.8.0+dfsg1-7+nmu1_mipsel.deb) ...
-Selecting previously unselected package libffi5:mipsel.
-Unpacking libffi5:mipsel (from .../libffi5_3.0.10-3_mipsel.deb) ...
-Selecting previously unselected package libglib2.0-0:mipsel.
-Unpacking libglib2.0-0:mipsel (from .../libglib2.0-0_2.33.12+really2.32.4-5_mipsel.deb) ...
-Selecting previously unselected package libcroco3:mipsel.
-Unpacking libcroco3:mipsel (from .../libcroco3_0.6.6-2_mipsel.deb) ...
-Selecting previously unselected package libunistring0:mipsel.
-Unpacking libunistring0:mipsel (from .../libunistring0_0.9.3-5_mipsel.deb) ...
-Selecting previously unselected package libgettextpo0:mipsel.
-Unpacking libgettextpo0:mipsel (from .../libgettextpo0_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_mipsel.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_mipsel.deb) ...
-Selecting previously unselected package libasprintf-dev:mipsel.
-Unpacking libasprintf-dev:mipsel (from .../libasprintf-dev_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package libgettextpo-dev:mipsel.
-Unpacking libgettextpo-dev:mipsel (from .../libgettextpo-dev_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_mipsel.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_mipsel.deb) ...
-Selecting previously unselected package libtinfo-dev:mipsel.
-Unpacking libtinfo-dev:mipsel (from .../libtinfo-dev_5.9-10_mipsel.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_mipsel.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:mipsel.
-Unpacking zlib1g-dev:mipsel (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_mipsel.deb) ...
-Setting up libpipeline1:mipsel (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:mipsel (0.18.1.1-10) ...
-Setting up libmagic1:mipsel (1:5.11-2.1) ...
-Setting up libpcre3:mipsel (1:8.31-2) ...
-Setting up libxml2:mipsel (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:mipsel (3.0.10-3) ...
-Setting up libglib2.0-0:mipsel (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:mipsel (0.6.6-2) ...
-Setting up libunistring0:mipsel (0.9.3-5) ...
-Setting up libgettextpo0:mipsel (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:mipsel (0.18.1.1-10) ...
-Setting up libgettextpo-dev:mipsel (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:mipsel (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:mipsel (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sb1-bcm91250a mipsel (mips64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1. [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture mipsel
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/misc'
-gcc -c -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-mipsel-muFrrg/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_mipsel.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_mipsel.deb'.
- dpkg-genchanges -B -mmipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org> >../samtools_0.1.19-1_mipsel.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0924
-
-samtools_0.1.19-1_mipsel.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: mipsel
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: mipsel Build Daemon (mayer) <buildd_mips-mayer at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 403caf7143bf1b0b949196cf55cbd1d1768f15d5 555674 samtools_0.1.19-1_mipsel.deb
- 271275f5ed7142222ac09a9549835fb3c72c542b 131464 libbam-dev_0.1.19-1_mipsel.deb
-Checksums-Sha256:
- 07ca0979fd1bb36fa4702e2f481309bf72b72e6634a306e5d3a8e9570509f099 555674 samtools_0.1.19-1_mipsel.deb
- 68096b1306f84e6e4014eaa37e6cb444cf51fc927245a65f88d793407cb82301 131464 libbam-dev_0.1.19-1_mipsel.deb
-Files:
- 44d1f7279db85e98bfe8666397f898ef 555674 science optional samtools_0.1.19-1_mipsel.deb
- 6d14454cb9202d9a7fcf084e040f43a8 131464 libdevel optional libbam-dev_0.1.19-1_mipsel.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_mipsel.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 555674 bytes: control archive= 1937 bytes.
- 32 bytes, 1 lines conffiles
- 793 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1439
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:23 ./
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/samtools/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:23 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 1966 2013-03-30 09:23 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:23 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:23 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/samtools/
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:24 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/bin/
--rwxr-xr-x root/root 176252 2013-03-30 09:24 ./usr/bin/bcftools
--rwxr-xr-x root/root 31780 2013-03-30 09:24 ./usr/bin/razip
--rwxr-xr-x root/root 483460 2013-03-30 09:24 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/samtools/
--rwxr-xr-x root/root 18508 2013-03-30 09:24 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 18192 2013-03-30 09:24 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 207416 2013-03-30 09:24 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 10032 2013-03-30 09:24 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 14224 2013-03-30 09:24 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 10068 2013-03-30 09:24 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:23 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_mipsel.deb
-──────────────────────────────
-
- new debian package, version 2.0.
- size 131464 bytes: control archive= 924 bytes.
- 713 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: mipsel
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 441
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
-drwxr-xr-x root/root 0 2013-03-30 09:24 ./usr/lib/
--rw-r--r-- root/root 328990 2013-03-30 09:24 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:23 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-mipsel-sbuild-ca64eee5-03d6-4a10-836c-decf0e5e9b54/build/buildd-samtools_0.1.19-1-mipsel-muFrrg
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following packages will be REMOVED:
- bash-completion* bsdmainutils* cdbs* debhelper* diffstat* file* gettext*
- gettext-base* groff-base* html2text* intltool-debian* libasprintf-dev*
- libasprintf0c2* libcroco3* libffi5* libgettextpo-dev* libgettextpo0*
- libglib2.0-0* libmagic1* libncurses5-dev* libpcre3* libpipeline1*
- libtinfo-dev* libunistring0* libxml2* man-db* po-debconf* quilt* zlib1g-dev*
-0 upgraded, 0 newly installed, 29 to remove and 2 not upgraded.
-After this operation, 30.2 MB disk space will be freed.
-(Reading database ... 13074 files and directories currently installed.)
-Removing bash-completion ...
-Purging configuration files for bash-completion ...
-Removing quilt ...
-Purging configuration files for quilt ...
-Removing debhelper ...
-Removing man-db ...
-Purging configuration files for man-db ...
-Removing bsdmainutils ...
-Purging configuration files for bsdmainutils ...
-Removing cdbs ...
-Removing diffstat ...
-Removing file ...
-Removing po-debconf ...
-Removing intltool-debian ...
-Removing gettext ...
-Removing gettext-base ...
-Removing groff-base ...
-Purging configuration files for groff-base ...
-Removing html2text ...
-Purging configuration files for html2text ...
-Removing libasprintf-dev:mipsel ...
-Removing libasprintf0c2:mipsel ...
-Removing libcroco3:mipsel ...
-Purging configuration files for libcroco3:mipsel ...
-Removing libglib2.0-0:mipsel ...
-Purging configuration files for libglib2.0-0:mipsel ...
-Removing libffi5:mipsel ...
-Purging configuration files for libffi5:mipsel ...
-Removing libgettextpo-dev:mipsel ...
-Removing libgettextpo0:mipsel ...
-Removing libmagic1:mipsel ...
-Purging configuration files for libmagic1:mipsel ...
-Removing libncurses5-dev ...
-Removing libpcre3:mipsel ...
-Purging configuration files for libpcre3:mipsel ...
-Removing libpipeline1:mipsel ...
-Purging configuration files for libpipeline1:mipsel ...
-Removing libtinfo-dev:mipsel ...
-Removing libunistring0:mipsel ...
-Purging configuration files for libunistring0:mipsel ...
-Removing libxml2:mipsel ...
-Purging configuration files for libxml2:mipsel ...
-Removing zlib1g-dev:mipsel ...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: mipsel
-Build-Space: 12852
-Build-Time: 342
-Distribution: sid
-Install-Time: 58
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 479
-Source-Version: 0.1.19-1
-Space: 12852
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0924
-Build needed 00:07:59, 12852k disc space
-Signature with key '4A2D13C7' requested:
-
diff --git a/kfreebsd-amd64.log b/mips64el.log
similarity index 55%
copy from kfreebsd-amd64.log
copy to mips64el.log
index 9c57b14..cd3f809 100644
--- a/kfreebsd-amd64.log
+++ b/mips64el.log
@@ -1,74 +1,45 @@
-From buildd at fano.debian.org Thu Sep 25 00:31:28 2014
-Return-path: <buildd at fano.debian.org>
-Received: from muffat.debian.org ([2607:f8f0:610:4000:6564:a62:ce0c:1392])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
- id 1XWwy0-0007ye-EG
- for logs at buildd.debian.org; Thu, 25 Sep 2014 00:31:28 +0000
-Received: from fano.debian.org ([2607:f8f0:610:4000:6564:a62:19:110])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=fano.debian.org, EMAIL=hostmaster at fano.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at fano.debian.org>)
- id 1XWwxy-0005aW-Mh; Thu, 25 Sep 2014 00:31:26 +0000
-Received: from buildd by fano.debian.org with local (Exim 4.80)
- (envelope-from <buildd at fano.debian.org>)
- id 1XWwxx-000Ir4-Vn; Thu, 25 Sep 2014 00:31:26 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 00:31:25 +0000
-From: buildd on fano <buildd at fano.debian.org>
-To: christoph at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_1.1-1 on kfreebsd-amd64
- (dist=sid)
-Key-Id: 8C5D26F3
-Message-Id: <E1XWwxx-000Ir4-Vn at fano.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on fano.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-manda-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (kfreebsd-amd64) 25 Sep 2014 00:27 ║
+║ samtools 1.2-3 (mips64el) 23 Sep 2015 01:48 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
-Machine Architecture: kfreebsd-amd64
-Host Architecture: kfreebsd-amd64
-Build Architecture: kfreebsd-amd64
+Machine Architecture: mipsel
+Host Architecture: mips64el
+Build Architecture: mips64el
-I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-wRcBJH' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ka-sbuild-1411604862-68022' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-PP85F4/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-PP85F4' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mips64el-sbuild-514192e8-3173-40d8-87da-bf80243c9a40' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://mirror-ubc.debian.org unstable InRelease [233 kB]
-Get:2 http://mirror-ubc.debian.org unstable/main Sources [9757 kB]
-Get:3 http://ftp.debian.org unstable InRelease [233 kB]
-Get:4 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:5 http://mirror-ubc.debian.org unstable/contrib Sources [67.0 kB]
-Get:6 http://mirror-ubc.debian.org unstable/non-free Sources [127 kB]
-Get:7 http://mirror-ubc.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
-Get:8 http://incoming.debian.org buildd-unstable/main Sources [450 kB]
-Get:9 http://ftp.debian.org unstable/main Sources [9757 kB]
-Get:10 http://mirror-ubc.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
-Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1082 B]
-Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [1643 B]
-Get:13 http://incoming.debian.org buildd-unstable/main kfreebsd-amd64 Packages [336 kB]
-Get:14 http://incoming.debian.org buildd-unstable/contrib kfreebsd-amd64 Packages [773 B]
-Get:15 http://ftp.debian.org unstable/contrib Sources [67.0 kB]
-Get:16 http://ftp.debian.org unstable/non-free Sources [127 kB]
-Get:17 http://ftp.debian.org unstable/main kfreebsd-amd64 Packages [8650 kB]
-Get:18 http://ftp.debian.org unstable/contrib kfreebsd-amd64 Packages [46.3 kB]
-Fetched 38.7 MB in 12s (3087 kB/s)
+Get:1 http://ftp.debian.org unstable InRelease [253 kB]
+Get:2 http://ftp.de.debian.org unstable InRelease [253 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.debian.org unstable/main Sources [8101 kB]
+Get:5 http://ftp.de.debian.org unstable/main Sources [8101 kB]
+Get:6 http://incoming.debian.org buildd-unstable/main Sources [401 kB]
+Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1812 B]
+Get:9 http://incoming.debian.org buildd-unstable/main mips64el Packages [356 kB]
+Get:10 http://incoming.debian.org buildd-unstable/contrib mips64el Packages [1216 B]
+Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:13 http://ftp.debian.org unstable/main mips64el Packages [5969 kB]
+Get:14 http://ftp.de.debian.org unstable/contrib Sources [59.7 kB]
+Get:15 http://ftp.de.debian.org unstable/non-free Sources [106 kB]
+Get:16 http://ftp.de.debian.org unstable/main mips64el Packages [5969 kB]
+Get:17 http://ftp.debian.org unstable/contrib mips64el Packages [28.0 kB]
+Get:18 http://ftp.de.debian.org unstable/contrib mips64el Packages [28.0 kB]
+Fetched 29.9 MB in 31s (940 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 5s (853 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 0s (6235 kB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-jaSah8/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-iDYCuv/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -116,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 38 not upgraded.
-Need to get 0 B/822 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 11 not upgraded.
+Need to get 0 B/772 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11188 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-1LN58k/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11696 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-iUt9l7/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -140,185 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5 libncurses5-dev libpipeline1 libtinfo-dev
- libtinfo5 libunistring0 libxml2 man-db ncurses-bin po-debconf tabix
- zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-The following packages will be upgraded:
- libncurses5 libtinfo5 ncurses-bin
-3 upgraded, 25 newly installed, 0 to remove and 35 not upgraded.
-Need to get 10.8 MB/10.8 MB of archives.
-After this operation, 30.2 MB of additional disk space will be used.
-Get:1 http://mirror-ubc.debian.org/debian/ unstable/main ncurses-bin kfreebsd-amd64 5.9+20140913-1 [347 kB]
-Get:2 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo5 kfreebsd-amd64 5.9+20140913-1 [283 kB]
-Get:3 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5 kfreebsd-amd64 5.9+20140913-1 [96.8 kB]
-Get:4 http://mirror-ubc.debian.org/debian/ unstable/main libpipeline1 kfreebsd-amd64 1.3.1-1 [26.6 kB]
-Get:5 http://mirror-ubc.debian.org/debian/ unstable/main groff-base kfreebsd-amd64 1.22.2-8 [1050 kB]
-Get:6 http://mirror-ubc.debian.org/debian/ unstable/main bsdmainutils kfreebsd-amd64 9.0.5 [211 kB]
-Get:7 http://mirror-ubc.debian.org/debian/ unstable/main man-db kfreebsd-amd64 2.7.0.1-1 [995 kB]
-Get:8 http://mirror-ubc.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:9 http://mirror-ubc.debian.org/debian/ unstable/main libasprintf0c2 kfreebsd-amd64 0.19.2-2 [30.8 kB]
-Get:10 http://mirror-ubc.debian.org/debian/ unstable/main libmagic1 kfreebsd-amd64 1:5.19-2 [238 kB]
-Get:11 http://mirror-ubc.debian.org/debian/ unstable/main libxml2 kfreebsd-amd64 2.9.1+dfsg1-4 [801 kB]
-Get:12 http://mirror-ubc.debian.org/debian/ unstable/main libffi6 kfreebsd-amd64 3.1-2 [19.3 kB]
-Get:13 http://mirror-ubc.debian.org/debian/ unstable/main libglib2.0-0 kfreebsd-amd64 2.42.0-1 [2480 kB]
-Get:14 http://mirror-ubc.debian.org/debian/ unstable/main libcroco3 kfreebsd-amd64 0.6.8-3 [134 kB]
-Get:15 http://mirror-ubc.debian.org/debian/ unstable/main libhts1 kfreebsd-amd64 1.1-1 [205 kB]
-Get:16 http://mirror-ubc.debian.org/debian/ unstable/main libunistring0 kfreebsd-amd64 0.9.3-5.2 [283 kB]
-Get:17 http://mirror-ubc.debian.org/debian/ unstable/main file kfreebsd-amd64 1:5.19-2 [58.2 kB]
-Get:18 http://mirror-ubc.debian.org/debian/ unstable/main gettext-base kfreebsd-amd64 0.19.2-2 [120 kB]
-Get:19 http://mirror-ubc.debian.org/debian/ unstable/main gettext kfreebsd-amd64 0.19.2-2 [1232 kB]
-Get:20 http://mirror-ubc.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:21 http://mirror-ubc.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:22 http://mirror-ubc.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:23 http://mirror-ubc.debian.org/debian/ unstable/main libhts-dev kfreebsd-amd64 1.1-1 [250 kB]
-Get:24 http://mirror-ubc.debian.org/debian/ unstable/main libtinfo-dev kfreebsd-amd64 5.9+20140913-1 [76.7 kB]
-Get:25 http://mirror-ubc.debian.org/debian/ unstable/main libncurses5-dev kfreebsd-amd64 5.9+20140913-1 [173 kB]
-Get:26 http://mirror-ubc.debian.org/debian/ unstable/main tabix kfreebsd-amd64 1.1-1 [190 kB]
-Get:27 http://mirror-ubc.debian.org/debian/ unstable/main zlib1g-dev kfreebsd-amd64 1:1.2.8.dfsg-2 [206 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 11 not upgraded.
+Need to get 18.0 MB/18.0 MB of archives.
+After this operation, 69.1 MB of additional disk space will be used.
+Get:1 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main libmagic1 mips64el 1:5.25-2 [255 kB]
+Get:3 http://ftp.de.debian.org/debian/ unstable/main groff-base mips64el 1.22.3-1+b1 [1279 kB]
+Get:4 http://incoming.debian.org/debian-buildd/ buildd-unstable/main file mips64el 1:5.25-2 [61.9 kB]
+Get:5 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils mips64el 9.0.6+b1 [188 kB]
+Get:6 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 mips64el 1.4.1-1+b1 [26.7 kB]
+Get:7 http://ftp.de.debian.org/debian/ unstable/main man-db mips64el 2.7.3-1 [988 kB]
+Get:8 http://ftp.de.debian.org/debian/ unstable/main libffi6 mips64el 3.2.1-3+b1 [20.8 kB]
+Get:9 http://ftp.de.debian.org/debian/ unstable/main gettext-base mips64el 0.19.6-1 [122 kB]
+Get:10 http://ftp.de.debian.org/debian/ unstable/main libicu55 mips64el 55.1-5 [7580 kB]
+Get:11 http://ftp.de.debian.org/debian/ unstable/main libxml2 mips64el 2.9.2+zdfsg1-4 [826 kB]
+Get:12 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 mips64el 2.44.1-1.1+b1 [2305 kB]
+Get:13 http://ftp.de.debian.org/debian/ unstable/main libcroco3 mips64el 0.6.8-3+b1 [123 kB]
+Get:14 http://ftp.de.debian.org/debian/ unstable/main libunistring0 mips64el 0.9.3-5.2+b1 [258 kB]
+Get:15 http://ftp.de.debian.org/debian/ unstable/main gettext mips64el 0.19.6-1 [1426 kB]
+Get:16 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://ftp.de.debian.org/debian/ unstable/main libhts1 mips64el 1.2.1-1 [213 kB]
+Get:20 http://ftp.de.debian.org/debian/ unstable/main libhts-dev mips64el 1.2.1-1 [303 kB]
+Get:21 http://ftp.de.debian.org/debian/ unstable/main libio-pty-perl mips64el 1:1.08-1 [33.2 kB]
+Get:22 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev mips64el 6.0+20150810-1+b1 [83.8 kB]
+Get:23 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev mips64el 6.0+20150810-1+b1 [182 kB]
+Get:24 http://ftp.de.debian.org/debian/ unstable/main tabix mips64el 1.2.1-1 [225 kB]
+Get:25 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev mips64el 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.8 MB in 0s (15.4 MB/s)
-(Reading database ... 11188 files and directories currently installed.)
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-Setting up ncurses-bin (5.9+20140913-1) ...
-(Reading database ... 11188 files and directories currently installed.)
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-Processing triggers for libc-bin (2.19-10) ...
-(Reading database ... 11188 files and directories currently installed.)
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-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:kfreebsd-amd64.
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-Unpacking libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
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-Unpacking libcroco3:kfreebsd-amd64 (0.6.8-3) ...
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-Unpacking libhts1:kfreebsd-amd64 (1.1-1) ...
-Selecting previously unselected package libunistring0:kfreebsd-amd64.
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-Unpacking libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
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-Unpacking file (1:5.19-2) ...
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-Unpacking gettext (0.19.2-2) ...
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-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:kfreebsd-amd64.
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-Unpacking libhts-dev:kfreebsd-amd64 (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:kfreebsd-amd64.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:kfreebsd-amd64.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_kfreebsd-amd64.deb ...
-Unpacking libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.1-1_kfreebsd-amd64.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:kfreebsd-amd64.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_kfreebsd-amd64.deb ...
-Unpacking zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:kfreebsd-amd64 (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:kfreebsd-amd64 (0.19.2-2) ...
-Setting up libmagic1:kfreebsd-amd64 (1:5.19-2) ...
-Setting up libxml2:kfreebsd-amd64 (2.9.1+dfsg1-4) ...
-Setting up libffi6:kfreebsd-amd64 (3.1-2) ...
-Setting up libglib2.0-0:kfreebsd-amd64 (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:kfreebsd-amd64 (0.6.8-3) ...
-Setting up libhts1:kfreebsd-amd64 (1.1-1) ...
-Setting up libunistring0:kfreebsd-amd64 (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:kfreebsd-amd64 (1.1-1) ...
-Setting up libtinfo-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Setting up libncurses5-dev:kfreebsd-amd64 (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:kfreebsd-amd64 (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-10) ...
+Fetched 18.0 MB in 3s (5872 kB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
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+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1+b1_mips64el.deb ...
+Unpacking groff-base (1.22.3-1+b1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6+b1_mips64el.deb ...
+Unpacking bsdmainutils (9.0.6+b1) ...
+Selecting previously unselected package libpipeline1:mips64el.
+Preparing to unpack .../libpipeline1_1.4.1-1+b1_mips64el.deb ...
+Unpacking libpipeline1:mips64el (1.4.1-1+b1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_mips64el.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:mips64el.
+Preparing to unpack .../libffi6_3.2.1-3+b1_mips64el.deb ...
+Unpacking libffi6:mips64el (3.2.1-3+b1) ...
+Selecting previously unselected package libmagic1:mips64el.
+Preparing to unpack .../libmagic1_1%3a5.25-2_mips64el.deb ...
+Unpacking libmagic1:mips64el (1:5.25-2) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-2_mips64el.deb ...
+Unpacking file (1:5.25-2) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_mips64el.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:mips64el.
+Preparing to unpack .../libicu55_55.1-5_mips64el.deb ...
+Unpacking libicu55:mips64el (55.1-5) ...
+Selecting previously unselected package libxml2:mips64el.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_mips64el.deb ...
+Unpacking libxml2:mips64el (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libglib2.0-0:mips64el.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1+b1_mips64el.deb ...
+Unpacking libglib2.0-0:mips64el (2.44.1-1.1+b1) ...
+Selecting previously unselected package libcroco3:mips64el.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_mips64el.deb ...
+Unpacking libcroco3:mips64el (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:mips64el.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_mips64el.deb ...
+Unpacking libunistring0:mips64el (0.9.3-5.2+b1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_mips64el.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:mips64el.
+Preparing to unpack .../libhts1_1.2.1-1_mips64el.deb ...
+Unpacking libhts1:mips64el (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:mips64el.
+Preparing to unpack .../libhts-dev_1.2.1-1_mips64el.deb ...
+Unpacking libhts-dev:mips64el (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1_mips64el.deb ...
+Unpacking libio-pty-perl (1:1.08-1) ...
+Selecting previously unselected package libtinfo-dev:mips64el.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1+b1_mips64el.deb ...
+Unpacking libtinfo-dev:mips64el (6.0+20150810-1+b1) ...
+Selecting previously unselected package libncurses5-dev:mips64el.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1+b1_mips64el.deb ...
+Unpacking libncurses5-dev:mips64el (6.0+20150810-1+b1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_mips64el.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1+b1) ...
+Setting up bsdmainutils (9.0.6+b1) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:mips64el (1.4.1-1+b1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:mips64el (3.2.1-3+b1) ...
+Setting up libmagic1:mips64el (1:5.25-2) ...
+Setting up file (1:5.25-2) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:mips64el (55.1-5) ...
+Setting up libxml2:mips64el (2.9.2+zdfsg1-4) ...
+Setting up libglib2.0-0:mips64el (2.44.1-1.1+b1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:mips64el (0.6.8-3+b1) ...
+Setting up libunistring0:mips64el (0.9.3-5.2+b1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:mips64el (1.2.1-1) ...
+Setting up libhts-dev:mips64el (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1) ...
+Setting up libtinfo-dev:mips64el (6.0+20150810-1+b1) ...
+Setting up libncurses5-dev:mips64el (6.0+20150810-1+b1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:mips64el (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: GNU/kFreeBSD 9.0-2-amd64 kfreebsd-amd64 (x86_64)
-Toolchain package versions: binutils_2.24.51.20140903-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-12 gcc-4.9_4.9.1-12 kfreebsd-kernel-headers_10.0~5 libc0.1-dev_2.19-10 libstdc++-4.9-dev_4.9.1-12 libstdc++6_4.9.1-12
-Package versions: apt_1.0.7 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140903-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-12 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils_4 [...]
+Kernel: Linux 4.1.0-0.bpo.1-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6+b1 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8+b1 coreutils_8.23-4+b1 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2+b1 dpkg-dev_1.18.2 e2fslibs_1.42.13-1+b1 e2fspro [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -329,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -348,16 +317,16 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=2
+DEB_BUILD_OPTIONS=parallel=5
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-SCHROOT_ALIAS_NAME=sid-kfreebsd-amd64-sbuild
-SCHROOT_CHROOT_NAME=sid-ka-sbuild
+SCHROOT_ALIAS_NAME=sid-mips64el-sbuild
+SCHROOT_CHROOT_NAME=sid-mips64el-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ka-sbuild-1411604862-68022
+SCHROOT_SESSION_ID=sid-mips64el-sbuild-514192e8-3173-40d8-87da-bf80243c9a40
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
@@ -367,16 +336,16 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
-dpkg-buildpackage: host architecture kfreebsd-amd64
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+ dpkg-source --before-build samtools-1.2
+dpkg-buildpackage: host architecture mips64el
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
- make -j2 distclean
+ make -j5 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
@@ -391,9 +360,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -409,12 +380,12 @@ dh build-arch --parallel
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_build -- \
HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a \
+ HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j2 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j5 HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
@@ -430,8 +401,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -476,118 +446,241 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-kfreebsd-gnu/libhts.a -lhts -lcu [...]
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lcurse [...]
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mips64el-linux-gnuabi64/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
make[1]: Entering directory '/«PKGBUILDDIR»'
dh_auto_test -- \
HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a \
+ HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j2 test HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j5 test HTSDIR=/usr/include HTSLIB=/usr/lib/mips64el-linux-gnuabi64/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/Ps_M93HaPJ/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/Ps_M93HaPJ/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/2K2PBSgp_6/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/Ps_M93HaPJ/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/2K2PBSgp_6/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/Ps_M93HaPJ/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/2K2PBSgp_6/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/Ps_M93HaPJ/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/Ps_M93HaPJ/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/2K2PBSgp_6/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/Ps_M93HaPJ/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/Ps_M93HaPJ/mpileup.bam.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.bam.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Ps_M93HaPJ/mpileup.bam.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/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/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/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/2K2PBSgp_6/mpileup.cram.list -f /tmp/2K2PBSgp_6/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/Ps_M93HaPJ/mpileup.cram.list -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ps_M93HaPJ/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/2K2PBSgp_6/mpileup.ref.fa.gz -r17:1050-1060 /tmp/2K2PBSgp_6/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/Ps_M93HaPJ/mpileup.ref.fa.gz -r17:1050-1060 /tmp/Ps_M93HaPJ/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
+.. ok
+
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
+
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
+.. ok
+
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
@@ -686,80 +779,80 @@ test_view:
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+ 55: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (SAM input).. ok
- 56: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (SAM input).. ok
- 57: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+ 57: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (BAM input).. ok
- 58: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (BAM input).. ok
+ 58: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (BAM input).. ok
- 59: Filter -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+ 59: Filter -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (CRAM input).. ok
- 60: Count -R /tmp/2K2PBSgp_6/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/Ps_M93HaPJ/view.001.fogn -r grp2 (CRAM input).. ok
- 61: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+ 61: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input).. ok
- 62: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (SAM input).. ok
+ 62: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (SAM input).. ok
- 63: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+ 63: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input).. ok
- 64: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (BAM input).. ok
- 65: Filter -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+ 65: Filter -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input).. ok
- 66: Count -r grp2 -R /tmp/2K2PBSgp_6/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/Ps_M93HaPJ/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test067.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/Ps_M93HaPJ/view.test067.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/Ps_M93HaPJ/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test069.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/Ps_M93HaPJ/view.test069.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/Ps_M93HaPJ/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/2K2PBSgp_6/view.test071.sam -h -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/Ps_M93HaPJ/view.test071.sam -h -l Library 2 /tmp/Ps_M93HaPJ/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/2K2PBSgp_6/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/Ps_M93HaPJ/view.test006.cram
.. expected failure
@@ -1142,37 +1235,41 @@ Samtools-htslib-API: bam_get_library() not yet implemented
260: Add @SQ with -T (BAM -> CRAM) .. ok
- 261: CIGAR B-operator removal .. ok
+ 261: Make CRAM with no UR field .. ok
+
+ 262: Decoding CRAM with no UR field via -T .. ok
- 262: Big SAM -> BAM .. ok
+ 263: CIGAR B-operator removal .. ok
- 263: Big SAM -> BAM (2 threads) .. ok
+ 264: Big SAM -> BAM .. ok
- 264: Big SAM -> BAM (4 threads) .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
- 265: Big SAM -> CRAM .. ok
+ 266: Big SAM -> BAM (4 threads) .. ok
- 266: Big SAM -> CRAM (2 threads) .. ok
+ 267: Big SAM -> CRAM .. ok
- 267: Big SAM -> CRAM (4 threads) .. ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
- 268: Subsample 0.2 (SAM input) ............ ok
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 269: Subsample 0.5 (SAM input) ............ ok
+ 270: Subsample 0.2 (SAM input) ............ ok
- 270: Subsample 0.8 (SAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
- 271: Subsample 0.2 (BAM input) ............ ok
+ 272: Subsample 0.8 (SAM input) ............ ok
- 272: Subsample 0.5 (BAM input) ............ ok
+ 273: Subsample 0.2 (BAM input) ............ ok
- 273: Subsample 0.8 (BAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
- 274: Subsample 0.2 (CRAM input) ............ ok
+ 275: Subsample 0.8 (BAM input) ............ ok
- 275: Subsample 0.5 (CRAM input) ............ ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1202,6 +1299,7 @@ test_cat:
test_bam2fq:
Generate BAM file .. ok
+Unsorted mode enabled
Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
@@ -1255,28 +1353,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/Ps_M93HaPJ/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/Ps_M93HaPJ/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/Ps_M93HaPJ/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/2K2PBSgp_6/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/Ps_M93HaPJ/depad.001p.bam
.. expected failure
@@ -1307,16 +1405,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 70698 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/j8G9qPU9yq
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/qbbLiy2S7U - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/sKujszcdjm - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1350,10 +1446,10 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 324
+ total .. 368
+ passed .. 336
failed .. 0
- expected failure .. 18
+ expected failure .. 32
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
@@ -1365,243 +1461,23 @@ Samtools mpileup tests:
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
-
-Expected passes: 123
-Unexpected passes: 0
-Expected failures: 1
-Unexpected failures: 0
-=> PASS
-test/split/test_count_rg
-test/split/test_expand_format_string
-test/split/test_filter_header_rg
-test/split/test_parse_args
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- fakeroot debian/rules binary-arch
-dh binary-arch --parallel
- dh_testroot -a -O--parallel
- dh_prep -a -O--parallel
- rm -f debian/samtools.substvars
- rm -f debian/samtools.*.debhelper
- rm -rf debian/samtools/
- debian/rules override_dh_auto_install
-make[1]: Entering directory '/«PKGBUILDDIR»'
-dh_auto_install -- \
- prefix=/usr \
- HTSDIR="/usr/include" \
- HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
- install -d debian/samtools
- make -j2 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-kfreebsd-gnu/libhts.a
-make[2]: Entering directory '/«PKGBUILDDIR»'
-mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
-install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
-install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make clean
-make[2]: Entering directory '/«PKGBUILDDIR»'
-rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
-cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
-rm -f *.o misc/*.o test/*.o test/*/*.o version.h
-rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
-make[2]: Leaving directory '/«PKGBUILDDIR»'
-make[1]: Leaving directory '/«PKGBUILDDIR»'
- dh_install -a -O--parallel
- install -d debian/samtools//usr
- cp -a debian/tmp/usr/bin debian/samtools//usr/
- install -d debian/samtools//usr/share/man
- cp -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
- dh_installdocs -a -O--parallel
- install -g 0 -o 0 -d debian/samtools/usr/share/doc/samtools
- cp -a AUTHORS debian/samtools/usr/share/doc/samtools
- cp -a debian/reference debian/samtools/usr/share/doc/samtools
- chown -R 0:0 debian/samtools/usr/share/doc
- chmod -R go=rX debian/samtools/usr/share/doc
- chmod -R u\+rw debian/samtools/usr/share/doc
- install -g 0 -o 0 -m 644 -p debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
- install -g 0 -o 0 -m 644 -p debian/copyright debian/samtools/usr/share/doc/samtools/copyright
- dh_installchangelogs -a -O--parallel
- install -o 0 -g 0 -p -m644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
- dh_installman -a -O--parallel
- man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
- chmod 644 samtools.1.new
- mv -f samtools.1.new samtools.1
- dh_perl -a -O--parallel
- (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
- mv debian/samtools.substvars.new debian/samtools.substvars
- dh_link -a -O--parallel
- dh_compress -a -O--parallel
- cd debian/samtools
- chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
- gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
- 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 644
- find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 755
- find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 644
- find debian/samtools/usr/lib/x86_64-kfreebsd-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
- find debian/samtools/usr/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
- dh_strip -a -O--parallel
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
- strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
- dh_makeshlibs -a -O--parallel
- rm -f debian/samtools/DEBIAN/shlibs
- dh_shlibdeps -a -O--parallel
- install -o 0 -g 0 -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/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short were not linked against libhts.so.1 (they use none of the library's symbols)
- dh_installdeb -a -O--parallel
- dh_gencontrol -a -O--parallel
- echo misc:Depends= >> debian/samtools.substvars
- dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
-dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
- chmod 644 debian/samtools/DEBIAN/control
- 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 644 debian/samtools/DEBIAN/md5sums
- chown 0:0 debian/samtools/DEBIAN/md5sums
- dh_builddeb -a -O--parallel
- dpkg-deb --build debian/samtools ..
-dpkg-deb: building package `samtools' in `../samtools_1.1-1_kfreebsd-amd64.deb'.
- dpkg-genchanges -B -mkfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano at buildd.debian.org> >../samtools_1.1-1_kfreebsd-amd64.changes
-dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
- dpkg-source --after-build samtools-1.1
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
-dpkg-buildpackage: binary-only upload (no source included)
+E: Caught signal ‘Terminated’: terminating immediately
+make[1]: *** wait: No child processes. Stop.
+make[1]: *** Waiting for unfinished jobs....
+make: *** wait: No child processes. Stop.
+make[1]: *** wait: No child processes. Stop.
+make[2]: *** [test] Terminated
+make: *** Waiting for unfinished jobs....
+make: *** wait: No child processes. Stop.
+Makefile:182: recipe for target 'test' failed
+Build killed with signal TERM after 150 minutes of inactivity
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0031
+Build finished at 20150923-0444
Finished
────────
-I: Built successfully
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build Chroot │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Changes │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_1.1-1_kfreebsd-amd64.changes:
-──────────────────────────────────────
-
-Format: 1.8
-Date: Thu, 25 Sep 2014 09:04:20 +0900
-Source: samtools
-Binary: samtools samtools-test
-Architecture: kfreebsd-amd64
-Version: 1.1-1
-Distribution: sid
-Urgency: medium
-Maintainer: kfreebsd-amd64 Build Daemon (fano) <buildd_kfreebsd-amd64-fano 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 (1.1-1) unstable; urgency=medium
- .
- c448d48 Merge tag '1.1' into debian/unstable
- d12ab1e Merge branch 'develop' into debian/unstable to solve issue
- with regression tests needing a pseudo-terminal.
- See https://github.com/samtools/samtools/issues/300
- c87f8ce Add autopkg tests.
- 7c50b7b Removed python-wrong-path-for-interpreter.patch
- (issue solved upstream).
-Checksums-Sha1:
- b6e1ad13e7adbb686479035064d939bc6b756735 376830 samtools_1.1-1_kfreebsd-amd64.deb
-Checksums-Sha256:
- 6ce726976ac08ee869cc1814cbc87d52d9efc7b6c2328daadc14e0cbf349cecb 376830 samtools_1.1-1_kfreebsd-amd64.deb
-Files:
- d0969c084ef2f415726914fc1baffe1d 376830 science optional samtools_1.1-1_kfreebsd-amd64.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_1.1-1_kfreebsd-amd64.deb
-─────────────────────────────────
-
- new debian package, version 2.0.
- size 376830 bytes: control archive=1566 bytes.
- 815 bytes, 16 lines control
- 1557 bytes, 27 lines md5sums
- Package: samtools
- Version: 1.1-1
- Architecture: kfreebsd-amd64
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1008
- Depends: libc0.1 (>= 2.17-91), libhts1 (>= 1.0), libncurses5 (>= 5.5-5~), libtinfo5, 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
- to retrieve reads in any regions swiftly. It is designed to work on a stream,
- and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
-
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/bin/
--rwxr-xr-x root/root 767928 2014-09-25 00:31 ./usr/bin/samtools
--rwxr-xr-x root/root 22664 2014-09-25 00:31 ./usr/bin/ace2sam
--rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-long
--rwxr-xr-x root/root 10336 2014-09-25 00:31 ./usr/bin/maq2sam-short
--rwxr-xr-x root/root 14440 2014-09-25 00:31 ./usr/bin/md5fa
--rwxr-xr-x root/root 10280 2014-09-25 00:31 ./usr/bin/md5sum-lite
--rwxr-xr-x root/root 22752 2014-09-25 00:31 ./usr/bin/wgsim
--rwxr-xr-x root/root 5328 2014-09-19 15:51 ./usr/bin/blast2sam.pl
--rwxr-xr-x root/root 3364 2014-09-19 15:51 ./usr/bin/bowtie2sam.pl
--rwxr-xr-x root/root 18032 2014-09-19 15:51 ./usr/bin/export2sam.pl
--rwxr-xr-x root/root 6125 2014-09-19 15:51 ./usr/bin/interpolate_sam.pl
--rwxr-xr-x root/root 6773 2014-09-19 15:51 ./usr/bin/novo2sam.pl
--rwxr-xr-x root/root 48023 2014-09-19 15:51 ./usr/bin/plot-bamstats
--rwxr-xr-x root/root 3208 2014-09-19 15:51 ./usr/bin/psl2sam.pl
--rwxr-xr-x root/root 8961 2014-09-19 15:51 ./usr/bin/sam2vcf.pl
--rwxr-xr-x root/root 16478 2014-09-19 15:51 ./usr/bin/samtools.pl
--rwxr-xr-x root/root 10789 2014-09-19 15:51 ./usr/bin/seq_cache_populate.pl
--rwxr-xr-x root/root 3909 2014-09-19 15:51 ./usr/bin/soap2sam.pl
--rwxr-xr-x root/root 7888 2014-09-19 15:51 ./usr/bin/varfilter.py
--rwxr-xr-x root/root 4157 2014-09-19 15:51 ./usr/bin/wgsim_eval.pl
--rwxr-xr-x root/root 3583 2014-09-19 15:51 ./usr/bin/zoom2sam.pl
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/man/man1/
--rw-r--r-- root/root 12774 2014-09-25 00:31 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/
-drwxr-xr-x root/root 0 2014-09-25 00:31 ./usr/share/doc/samtools/
--rw-r--r-- root/root 828 2014-09-19 15:51 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2014-09-24 23:56 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1031 2014-09-24 23:56 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 3462 2014-09-24 23:56 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 3270 2014-09-25 00:05 ./usr/share/doc/samtools/changelog.Debian.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
+E: Build failure (dpkg-buildpackage died)
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1614,24 +1490,21 @@ Not cleaning session: cloned chroot in use
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
-Build Architecture: kfreebsd-amd64
-Build-Space: 15254
-Build-Time: 132
+Build Architecture: mips64el
+Build-Space: 57712
+Build-Time: 10385
Distribution: sid
-Host Architecture: kfreebsd-amd64
-Install-Time: 32
-Job: samtools_1.1-1
-Machine Architecture: kfreebsd-amd64
+Fail-Stage: build
+Host Architecture: mips64el
+Install-Time: 57
+Job: samtools_1.2-3
+Machine Architecture: mipsel
Package: samtools
-Package-Time: 217
-Source-Version: 1.1-1
-Space: 15254
-Status: successful
-Version: 1.1-1
+Package-Time: 10531
+Source-Version: 1.2-3
+Space: 57712
+Status: attempted
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0031
-Build needed 00:03:37, 15254k disc space
-Signature with key '8C5D26F3' requested:
- signfile /home/buildd/build/samtools_1.1-1_kfreebsd-amd64.changes 8C5D26F3
-
-Successfully signed changes file
+Finished at 20150923-0444
+Build needed 02:55:31, 57712k disc space
diff --git a/mipsel.log b/mipsel.log
index 265c1be..b9ae932 100644
--- a/mipsel.log
+++ b/mipsel.log
@@ -1,74 +1,45 @@
-From buildd at eysler.debian.org Thu Sep 25 02:28:22 2014
-Return-path: <buildd at eysler.debian.org>
-Received: from mailly.debian.org ([2001:41b8:202:deb:6564:a62:52c3:4b72])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=mailly.debian.org, EMAIL=hostmaster at mailly.debian.org (verified)
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at eysler.debian.org>)
- id 1XWyn8-0000BE-Px
- for logs at buildd.debian.org; Thu, 25 Sep 2014 02:28:22 +0000
-Received: from eysler.debian.org ([2001:858:2:2:1a1a:0:563b:7698])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=eysler.debian.org, EMAIL=hostmaster at eysler.debian.org (verified)
- by mailly.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at eysler.debian.org>)
- id 1XWyn7-0003gc-HB
- for logs at buildd.debian.org; Thu, 25 Sep 2014 02:28:22 +0000
-Received: from buildd by eysler.debian.org with local (Exim 4.80)
- (envelope-from <buildd at eysler.debian.org>) id 1XWyn4-0002Hb-Io
- for logs at buildd.debian.org; Thu, 25 Sep 2014 02:28:18 +0000
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.028 (F2.82; B3.13; Q3.13)
-Date: Thu, 25 Sep 2014 02:28:17 +0000
-From: buildd on eysler <buildd at eysler.debian.org>
-To: logs at buildd.debian.org
-Subject: Log for attempted build of samtools_1.1-1 on mipsel (dist=sid)
-Key-Id: F6A5E741
-Message-Id: <E1XWyn4-0002Hb-Io at eysler.debian.org>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on eysler.debian.org
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on mipsel-aql-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (mipsel) 25 Sep 2014 02:09 ║
+║ samtools 1.2-3 (mipsel) 22 Sep 2015 16:19 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
Machine Architecture: mipsel
Host Architecture: mipsel
Build Architecture: mipsel
-I: NOTICE: Log filtering will replace 'build/samtools-WhGDgZ/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-WhGDgZ' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-9da2abb3-05c8-4f5b-adf5-e24ce4b9aa67' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-B_M8Do/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-B_M8Do' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-mipsel-sbuild-af2c7f8d-0e84-4285-9965-6f83ee9596f6' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.at.debian.org unstable InRelease [233 kB]
-Get:2 http://ftp.debian.org unstable InRelease [233 kB]
-Get:3 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:4 http://ftp.at.debian.org unstable/main Sources [7548 kB]
-Get:5 http://incoming.debian.org buildd-unstable/main Sources [357 kB]
-Get:6 http://ftp.debian.org unstable/main Sources [7548 kB]
-Get:7 http://incoming.debian.org buildd-unstable/contrib Sources [776 B]
-Get:8 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
-Get:9 http://incoming.debian.org buildd-unstable/main mipsel Packages [282 kB]
-Get:10 http://incoming.debian.org buildd-unstable/contrib mipsel Packages [556 B]
-Get:11 http://ftp.at.debian.org unstable/contrib Sources [57.1 kB]
-Get:12 http://ftp.at.debian.org unstable/non-free Sources [107 kB]
-Get:13 http://ftp.at.debian.org unstable/main mipsel Packages [6816 kB]
-Get:14 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
-Get:15 http://ftp.debian.org unstable/non-free Sources [107 kB]
-Get:16 http://ftp.debian.org unstable/main mipsel Packages [6816 kB]
-Get:17 http://ftp.at.debian.org unstable/contrib mipsel Packages [40.6 kB]
-Get:18 http://ftp.debian.org unstable/contrib mipsel Packages [40.6 kB]
-Fetched 30.4 MB in 1min 14s (405 kB/s)
+Get:1 http://ftp.uk.debian.org unstable InRelease [253 kB]
+Get:2 http://ftp.debian.org unstable InRelease [253 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:4 http://incoming.debian.org buildd-unstable/main Sources [354 kB]
+Get:5 http://ftp.uk.debian.org unstable/main Sources [8093 kB]
+Get:6 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:7 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
+Get:8 http://incoming.debian.org buildd-unstable/main mipsel Packages [98.7 kB]
+Get:9 http://incoming.debian.org buildd-unstable/contrib mipsel Packages [1060 B]
+Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:11 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:12 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:13 http://ftp.uk.debian.org unstable/contrib Sources [59.7 kB]
+Get:14 http://ftp.uk.debian.org unstable/non-free Sources [106 kB]
+Get:15 http://ftp.debian.org unstable/main mipsel Packages [7352 kB]
+Get:16 http://ftp.uk.debian.org unstable/main mipsel Packages [7352 kB]
+Get:17 http://ftp.debian.org unstable/contrib mipsel Packages [44.3 kB]
+Get:18 http://ftp.uk.debian.org unstable/contrib mipsel Packages [44.3 kB]
+Fetched 32.4 MB in 49s (648 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -89,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 1s (2765 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 0s (4824 kB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-FlpToU/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-MvnuoI/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -116,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
-Need to get 0 B/816 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 10557 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-2j5g5j/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11666 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-RPeFbc/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -139,158 +124,171 @@ Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
- bash-completion debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf tabix zlib1g-dev
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- dh-make gettext-doc groff ncurses-doc less www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
- bash-completion debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy tabix
- zlib1g-dev
-0 upgraded, 24 newly installed, 0 to remove and 1 not upgraded.
-Need to get 9511 kB/9512 kB of archives.
-After this operation, 30.5 MB of additional disk space will be used.
-Get:1 http://ftp.at.debian.org/debian/ unstable/main libpipeline1 mipsel 1.3.1-1 [23.5 kB]
-Get:2 http://ftp.at.debian.org/debian/ unstable/main groff-base mipsel 1.22.2-8 [1147 kB]
-Get:3 http://ftp.at.debian.org/debian/ unstable/main man-db mipsel 2.7.0.1-1 [981 kB]
-Get:4 http://ftp.at.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:5 http://ftp.at.debian.org/debian/ unstable/main libasprintf0c2 mipsel 0.19.2-2 [30.7 kB]
-Get:6 http://ftp.at.debian.org/debian/ unstable/main libmagic1 mipsel 1:5.19-2 [237 kB]
-Get:7 http://ftp.at.debian.org/debian/ unstable/main libxml2 mipsel 2.9.1+dfsg1-4 [710 kB]
-Get:8 http://ftp.at.debian.org/debian/ unstable/main libffi6 mipsel 3.1-2 [17.9 kB]
-Get:9 http://ftp.at.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.42.0-1 [2300 kB]
-Get:10 http://ftp.at.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.8-3 [119 kB]
-Get:11 http://ftp.at.debian.org/debian/ unstable/main libhts1 mipsel 1.1-1 [185 kB]
-Get:12 http://ftp.at.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5.2 [260 kB]
-Get:13 http://ftp.at.debian.org/debian/ unstable/main file mipsel 1:5.19-2 [58.0 kB]
-Get:14 http://ftp.at.debian.org/debian/ unstable/main gettext-base mipsel 0.19.2-2 [119 kB]
-Get:15 http://ftp.at.debian.org/debian/ unstable/main gettext mipsel 0.19.2-2 [1181 kB]
-Get:16 http://ftp.at.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:17 http://ftp.at.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:18 http://ftp.at.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:19 http://ftp.at.debian.org/debian/ unstable/main libhts-dev mipsel 1.1-1 [259 kB]
-Get:20 http://ftp.at.debian.org/debian/ unstable/main libtinfo-dev mipsel 5.9+20140913-1 [77.0 kB]
-Get:21 http://ftp.at.debian.org/debian/ unstable/main libncurses5-dev mipsel 5.9+20140913-1 [173 kB]
-Get:22 http://ftp.at.debian.org/debian/ unstable/main tabix mipsel 1.1-1 [184 kB]
-Get:23 http://ftp.at.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.8.dfsg-2 [204 kB]
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 17.8 MB/17.8 MB of archives.
+After this operation, 66.5 MB of additional disk space will be used.
+Get:1 http://ftp.uk.debian.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://ftp.uk.debian.org/debian/ unstable/main groff-base mipsel 1.22.3-1 [1218 kB]
+Get:3 http://ftp.uk.debian.org/debian/ unstable/main bsdmainutils mipsel 9.0.6 [184 kB]
+Get:4 http://ftp.uk.debian.org/debian/ unstable/main libpipeline1 mipsel 1.4.1-1 [26.9 kB]
+Get:5 http://ftp.uk.debian.org/debian/ unstable/main man-db mipsel 2.7.3-1 [988 kB]
+Get:6 http://ftp.uk.debian.org/debian/ unstable/main libffi6 mipsel 3.2.1-3 [18.4 kB]
+Get:7 http://ftp.uk.debian.org/debian/ unstable/main libglib2.0-0 mipsel 2.44.1-1.1 [2294 kB]
+Get:8 http://ftp.uk.debian.org/debian/ unstable/main libicu55 mipsel 55.1-5 [7567 kB]
+Get:9 http://ftp.uk.debian.org/debian/ unstable/main libxml2 mipsel 2.9.2+zdfsg1-4 [824 kB]
+Get:10 http://ftp.uk.debian.org/debian/ unstable/main libcroco3 mipsel 0.6.8-3+b1 [119 kB]
+Get:11 http://ftp.uk.debian.org/debian/ unstable/main libunistring0 mipsel 0.9.3-5.2+b1 [257 kB]
+Get:12 http://ftp.uk.debian.org/debian/ unstable/main libmagic1 mipsel 1:5.25-1 [258 kB]
+Get:13 http://ftp.uk.debian.org/debian/ unstable/main file mipsel 1:5.25-1 [61.6 kB]
+Get:14 http://ftp.uk.debian.org/debian/ unstable/main gettext-base mipsel 0.19.6-1 [120 kB]
+Get:15 http://ftp.uk.debian.org/debian/ unstable/main gettext mipsel 0.19.6-1 [1413 kB]
+Get:16 http://ftp.uk.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://ftp.uk.debian.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://ftp.uk.debian.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://ftp.uk.debian.org/debian/ unstable/main libhts1 mipsel 1.2.1-1 [211 kB]
+Get:20 http://ftp.uk.debian.org/debian/ unstable/main libhts-dev mipsel 1.2.1-1 [291 kB]
+Get:21 http://ftp.uk.debian.org/debian/ unstable/main libio-pty-perl mipsel 1:1.08-1+b4 [33.6 kB]
+Get:22 http://ftp.uk.debian.org/debian/ unstable/main libtinfo-dev mipsel 6.0+20150810-1 [78.5 kB]
+Get:23 http://ftp.uk.debian.org/debian/ unstable/main libncurses5-dev mipsel 6.0+20150810-1 [173 kB]
+Get:24 http://ftp.uk.debian.org/debian/ unstable/main tabix mipsel 1.2.1-1 [220 kB]
+Get:25 http://ftp.uk.debian.org/debian/ unstable/main zlib1g-dev mipsel 1:1.2.8.dfsg-2+b1 [205 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9511 kB in 3s (2481 kB/s)
-Selecting previously unselected package libpipeline1:mipsel.
-(Reading database ... 10557 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_mipsel.deb ...
-Unpacking libpipeline1:mipsel (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_mipsel.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_mipsel.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:mipsel.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_mipsel.deb ...
-Unpacking libasprintf0c2:mipsel (0.19.2-2) ...
-Selecting previously unselected package libmagic1:mipsel.
-Preparing to unpack .../libmagic1_1%3a5.19-2_mipsel.deb ...
-Unpacking libmagic1:mipsel (1:5.19-2) ...
-Selecting previously unselected package libxml2:mipsel.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4_mipsel.deb ...
-Unpacking libxml2:mipsel (2.9.1+dfsg1-4) ...
-Selecting previously unselected package libffi6:mipsel.
-Preparing to unpack .../libffi6_3.1-2_mipsel.deb ...
-Unpacking libffi6:mipsel (3.1-2) ...
-Selecting previously unselected package libglib2.0-0:mipsel.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_mipsel.deb ...
-Unpacking libglib2.0-0:mipsel (2.42.0-1) ...
-Selecting previously unselected package libcroco3:mipsel.
-Preparing to unpack .../libcroco3_0.6.8-3_mipsel.deb ...
-Unpacking libcroco3:mipsel (0.6.8-3) ...
-Selecting previously unselected package libhts1:mipsel.
-Preparing to unpack .../libhts1_1.1-1_mipsel.deb ...
-Unpacking libhts1:mipsel (1.1-1) ...
-Selecting previously unselected package libunistring0:mipsel.
-Preparing to unpack .../libunistring0_0.9.3-5.2_mipsel.deb ...
-Unpacking libunistring0:mipsel (0.9.3-5.2) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2_mipsel.deb ...
-Unpacking file (1:5.19-2) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_mipsel.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_mipsel.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:mipsel.
-Preparing to unpack .../libhts-dev_1.1-1_mipsel.deb ...
-Unpacking libhts-dev:mipsel (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:mipsel.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_mipsel.deb ...
-Unpacking libtinfo-dev:mipsel (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:mipsel.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_mipsel.deb ...
-Unpacking libncurses5-dev:mipsel (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.1-1_mipsel.deb ...
-Unpacking tabix (1.1-1) ...
-Selecting previously unselected package zlib1g-dev:mipsel.
-Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2_mipsel.deb ...
-Unpacking zlib1g-dev:mipsel (1:1.2.8.dfsg-2) ...
-Selecting previously unselected package sbuild-build-depends-samtools-dummy.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:mipsel (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:mipsel (0.19.2-2) ...
-Setting up libmagic1:mipsel (1:5.19-2) ...
-Setting up libxml2:mipsel (2.9.1+dfsg1-4) ...
-Setting up libffi6:mipsel (3.1-2) ...
-Setting up libglib2.0-0:mipsel (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:mipsel (0.6.8-3) ...
-Setting up libhts1:mipsel (1.1-1) ...
-Setting up libunistring0:mipsel (0.9.3-5.2) ...
-Setting up file (1:5.19-2) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:mipsel (1.1-1) ...
-Setting up libtinfo-dev:mipsel (5.9+20140913-1) ...
-Setting up libncurses5-dev:mipsel (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Fetched 17.8 MB in 3s (4600 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%
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(Reading database ... 55%
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11666 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_mipsel.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_mipsel.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:mipsel.
+Preparing to unpack .../libpipeline1_1.4.1-1_mipsel.deb ...
+Unpacking libpipeline1:mipsel (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_mipsel.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:mipsel.
+Preparing to unpack .../libffi6_3.2.1-3_mipsel.deb ...
+Unpacking libffi6:mipsel (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:mipsel.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_mipsel.deb ...
+Unpacking libglib2.0-0:mipsel (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:mipsel.
+Preparing to unpack .../libicu55_55.1-5_mipsel.deb ...
+Unpacking libicu55:mipsel (55.1-5) ...
+Selecting previously unselected package libxml2:mipsel.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_mipsel.deb ...
+Unpacking libxml2:mipsel (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:mipsel.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_mipsel.deb ...
+Unpacking libcroco3:mipsel (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:mipsel.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_mipsel.deb ...
+Unpacking libunistring0:mipsel (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:mipsel.
+Preparing to unpack .../libmagic1_1%3a5.25-1_mipsel.deb ...
+Unpacking libmagic1:mipsel (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_mipsel.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_mipsel.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_mipsel.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:mipsel.
+Preparing to unpack .../libhts1_1.2.1-1_mipsel.deb ...
+Unpacking libhts1:mipsel (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:mipsel.
+Preparing to unpack .../libhts-dev_1.2.1-1_mipsel.deb ...
+Unpacking libhts-dev:mipsel (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b4_mipsel.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b4) ...
+Selecting previously unselected package libtinfo-dev:mipsel.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_mipsel.deb ...
+Unpacking libtinfo-dev:mipsel (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:mipsel.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_mipsel.deb ...
+Unpacking libncurses5-dev:mipsel (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_mipsel.deb ...
+Unpacking tabix (1.2.1-1) ...
+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) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:mipsel (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:mipsel (3.2.1-3) ...
+Setting up libglib2.0-0:mipsel (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:mipsel (55.1-5) ...
+Setting up libxml2:mipsel (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:mipsel (0.6.8-3+b1) ...
+Setting up libunistring0:mipsel (0.9.3-5.2+b1) ...
+Setting up libmagic1:mipsel (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:mipsel (1.2.1-1) ...
+Setting up libhts-dev:mipsel (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b4) ...
+Setting up libtinfo-dev:mipsel (6.0+20150810-1) ...
+Setting up libncurses5-dev:mipsel (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:mipsel (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.14-0.bpo.2-loongson-2e mipsel (mips64)
-Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-2
-Package versions: apt_1.0.9.1 base-files_7.5 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.8 build-essential_11.7 bzip2_1.0.6-7 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4 debconf_1.5.53 debfoster_2.7-2 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.13 dpkg-dev_1.17.13 e2fslibs_1.42.12-1 e2fsprogs_1.42.12-1 fakeroot_1.20.1-1.1 file_1:5.19-2 findutils [...]
+Kernel: Linux 3.16.0-4-loongson-3 mipsel (mips64)
+Toolchain package versions: binutils_2.25.1-2 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-2 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b1 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -301,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -320,6 +317,7 @@ Sufficient free space for build
User Environment
────────────────
+DEB_BUILD_OPTIONS=parallel=5
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
@@ -328,26 +326,27 @@ SCHROOT_CHROOT_NAME=sid-mipsel-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-mipsel-sbuild-9da2abb3-05c8-4f5b-adf5-e24ce4b9aa67
+SCHROOT_SESSION_ID=sid-mipsel-sbuild-af2c7f8d-0e84-4285-9965-6f83ee9596f6
SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
+USERNAME=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture mipsel
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
- make -j1 distclean
+ make -j5 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
@@ -362,9 +361,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -385,100 +386,84 @@ dh_auto_build -- \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a "CFLAGS=-g -O2 -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j5 HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
-padding.c: In function 'bam_pad2unpad':
-padding.c:199:17: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat=]
- fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %d in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
- ^
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lcurse [...]
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
-misc/ace2sam.c: In function 'main':
-misc/ace2sam.c:112:13: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat=]
- fprintf(stderr, "H @SQ\tSN:%s\tLN:%ld\n", t[0].s, t[is_padded?1:2].l); // The SAM header line
- ^
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
-test/merge/test_rtrans_build.c: In function 'main':
-test/merge/test_rtrans_build.c:79:29: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMIC_SEED = 0x1234abcd330e;
- ^
gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
-test/merge/test_trans_tbl_init.c: In function 'main':
-test/merge/test_trans_tbl_init.c:323:31: warning: overflow in implicit constant conversion [-Woverflow]
- const long GIMMICK_SEED = 0x1234abcd330e;
- ^
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
-gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
-gcc -g -O2 -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lcurses -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/mipsel-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -487,251 +472,265 @@ dh_auto_test -- \
HTSDIR="/usr/include" \
HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j5 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/ThgE2wBlHt/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/xlCscIPJVB/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/ThgE2wBlHt/bgzip.dat.gz
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/xlCscIPJVB/bgzip.dat.gz
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/ThgE2wBlHt/bgzip.dat.gz
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/xlCscIPJVB/bgzip.dat.gz
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 3:11-13 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 2:998-1003 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 1:100-104 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
-/«PKGBUILDDIR»/samtools faidx /tmp/ThgE2wBlHt/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+/«PKGBUILDDIR»/samtools faidx /tmp/xlCscIPJVB/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
- /«PKGBUILDDIR»/samtools index /tmp/ThgE2wBlHt/large_chrom.bam
+ /«PKGBUILDDIR»/samtools index /tmp/xlCscIPJVB/large_chrom.bam
.. expected failure
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/ThgE2wBlHt/large_chrom.bam ref2
-
- The outputs stdout differ:
- /«PKGBUILDDIR»/test/dat/large_chrom.out
- /«PKGBUILDDIR»/test/dat/large_chrom.out.new
-.. expected failure
+ /«PKGBUILDDIR»/samtools view /tmp/xlCscIPJVB/large_chrom.bam ref2
+.. ok
test_index:
- /«PKGBUILDDIR»/samtools view /tmp/ThgE2wBlHt/large_chrom.bam ref2:1-541556283
+ /«PKGBUILDDIR»/samtools view /tmp/xlCscIPJVB/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/ThgE2wBlHt/mpileup.bam.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/xlCscIPJVB/mpileup.bam.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-150
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ThgE2wBlHt/mpileup.bam.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xlCscIPJVB/mpileup.bam.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/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/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/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/ThgE2wBlHt/mpileup.cram.list -f /tmp/ThgE2wBlHt/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/xlCscIPJVB/mpileup.cram.list -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ThgE2wBlHt/mpileup.1.bam | grep -v mpileup
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xlCscIPJVB/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
- /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/ThgE2wBlHt/mpileup.ref.fa.gz -r17:1050-1060 /tmp/ThgE2wBlHt/mpileup.1.cram | grep -v mpileup
-test/test.pl: module IO::Pty not found; skipping usage tests
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xlCscIPJVB/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xlCscIPJVB/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
-test_view:
- Generating test data file .................. done
- 1: SAM -> BAM -> SAM
- SAM files differ at /tmp/ThgE2wBlHt/view.test001.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test001.bam -b /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test001.bam.sam /tmp/ThgE2wBlHt/view.test001.bam
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+test_usage_subcommand:
+ samtools faidx
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 2: SAM -> uncompressed BAM .. ok
+test_usage_subcommand:
+ samtools index
+.. ok
- 3: uncompressed BAM -> SAM and compare
- SAM files differ at /tmp/ThgE2wBlHt/view.test003.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test003.sam -h /tmp/ThgE2wBlHt/view.test002.bam
+test_usage_subcommand:
+ samtools calmd
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools fixmate
+.. ok
- 4: SAM -> fast compressed BAM .. ok
+test_usage_subcommand:
+ samtools reheader
- 5: fast compressed BAM -> SAM and compare
- SAM files differ at /tmp/ThgE2wBlHt/view.test005.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test005.sam -h /tmp/ThgE2wBlHt/view.test004.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools rmdup
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 6: SAM -> CRAM -> SAM (UR header tags)
- SAM files differ at /tmp/ThgE2wBlHt/view.test006.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test006.cram -C /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test006.cram.sam /tmp/ThgE2wBlHt/view.test006.cram
+test_usage_subcommand:
+ samtools targetcut
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools bamshuf
- 7: SAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/ThgE2wBlHt/view.test007.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test007.cram -C /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test007.cram.sam /tmp/ThgE2wBlHt/view.test007.cram
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools cat
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 8: BAM -> CRAM with UR -> SAM
- SAM files differ at /tmp/ThgE2wBlHt/view.test008.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test008.cram -C /tmp/ThgE2wBlHt/view.test001.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test008.cram.sam /tmp/ThgE2wBlHt/view.test008.cram
+test_usage_subcommand:
+ samtools merge
+.. ok
+test_usage_subcommand:
+ samtools mpileup
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 9: SAM -> BAM (M5 header tags)
- SAM files differ at /tmp/ThgE2wBlHt/view.test009.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test009.bam -b /«PKGBUILDDIR»/test/dat/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test009.bam.sam /tmp/ThgE2wBlHt/view.test009.bam
+test_usage_subcommand:
+ samtools sort
+.. ok
+test_usage_subcommand:
+ samtools split
+.. ok
-.. failed ...
+test_usage_subcommand:
+ samtools bam2fq
+.. ok
- 10: SAM -> BAM -> CRAM -> SAM (M5 header tags)
- SAM files differ at /tmp/ThgE2wBlHt/view.test010.cram.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test010.cram -C /tmp/ThgE2wBlHt/view.test009.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test010.cram.sam /tmp/ThgE2wBlHt/view.test010.cram
+test_usage_subcommand:
+ samtools bedcov
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools depth
- 11: CRAM -> BAM with UR
- SAM files differ at /tmp/ThgE2wBlHt/view.test011.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test011.bam -b /tmp/ThgE2wBlHt/view.test008.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test011.bam.sam /tmp/ThgE2wBlHt/view.test011.bam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools flagstat
-.. failed ...
+ Usage on stderr rather than stdout
+.. expected failure
- 12: CRAM -> BAM with M5
- SAM files differ at /tmp/ThgE2wBlHt/view.test012.bam.sam : 34 / /«PKGBUILDDIR»/test/dat/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test012.bam -b /tmp/ThgE2wBlHt/view.test010.cram && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test012.bam.sam /tmp/ThgE2wBlHt/view.test012.bam
+test_usage_subcommand:
+ samtools idxstats
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools phase
- 13: SAM -> SAM via stdout
- SAM files differ at /tmp/ThgE2wBlHt/view.test013.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/view.001.sam
+ Usage on stderr rather than stdout
+.. expected failure
+test_usage_subcommand:
+ samtools stats
+.. ok
-.. failed ...
+test_usage_subcommand:
+ samtools flags
- 14: SAM -> BAM via stdout .. ok
+ Usage on stderr rather than stdout
+.. expected failure
- 15: SAM -> CRAM via stdout
- SAM files differ at /tmp/ThgE2wBlHt/view.test015.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -C /tmp/ThgE2wBlHt/view.001.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test015.cram.sam /tmp/ThgE2wBlHt/view.test015.cram
+test_usage_subcommand:
+ samtools tview
+ Usage on stderr rather than stdout
+.. expected failure
-.. failed ...
+test_usage_subcommand:
+ samtools view
- 16: SAM from stdin -> SAM
- SAM files differ at /tmp/ThgE2wBlHt/view.test016.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test016.sam -h -
+ Usage on stderr rather than stdout
+.. expected failure
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
-.. failed ...
+ 2: SAM -> uncompressed BAM .. ok
- 17: BAM from stdin -> SAM
- SAM files differ at /tmp/ThgE2wBlHt/view.test017.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test017.sam -h -
+ 3: uncompressed BAM -> SAM and compare .. ok
+ 4: SAM -> fast compressed BAM .. ok
-.. failed ...
+ 5: fast compressed BAM -> SAM and compare .. ok
- 18: CRAM from stdin -> SAM
- SAM files differ at /tmp/ThgE2wBlHt/view.test018.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test018.sam -h -
+ 6: SAM -> CRAM -> SAM (UR header tags) .. ok
+ 7: SAM -> CRAM -> SAM (M5 header tags) .. ok
-.. failed ...
+ 8: BAM -> CRAM with UR -> SAM .. ok
- 19: samtools view -H (SAM input) .. ok
+ 9: SAM -> BAM (M5 header tags) .. ok
- 20: samtools view -H (BAM input) .. ok
+ 10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
- 21: samtools view -H (CRAM input) .. 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
- 22: No headers (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test022.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test022.body /tmp/ThgE2wBlHt/view.001.sam
+ 15: SAM -> CRAM via stdout .. ok
+ 16: SAM from stdin -> SAM .. ok
-.. failed ...
+ 17: BAM from stdin -> SAM .. ok
- 23: No headers (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test023.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test023.body /tmp/ThgE2wBlHt/view.test001.bam
+ 18: CRAM from stdin -> SAM .. ok
+ 19: samtools view -H (SAM input) .. ok
+
+ 20: samtools view -H (BAM input) .. ok
-.. failed ...
+ 21: samtools view -H (CRAM input) .. ok
- 24: No headers (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test024.body : 6 / /tmp/ThgE2wBlHt/view.001.body.sam : 6
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test024.body /tmp/ThgE2wBlHt/view.test006.cram
+ 22: No headers (SAM input) .. ok
+ 23: No headers (BAM input) .. ok
-.. failed ...
+ 24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
@@ -745,206 +744,116 @@ test_view:
30: Count -f 128 (CRAM input) .. ok
- 31: Filter -F 128 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test031.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test031.sam -h -F 128 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
- 33: Filter -F 128 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test033.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test033.sam -h -F 128 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
- 35: Filter -F 128 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test035.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test035.sam -h -F 128 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
- 37: Filter -F 128 -f 2 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test037.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test037.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/ThgE2wBlHt/view.test039.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test039.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 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)
- SAM files differ at /tmp/ThgE2wBlHt/view.test041.sam : 34 / /tmp/ThgE2wBlHt/view.001.rej128req2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test041.sam -h -F 128 -f 2 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
- 43: Filter -r grp2 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test043.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test043.sam -h -r grp2 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
- 45: Filter -r grp2 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test045.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test045.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
- 47: Filter -r grp2 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test047.sam : 29 / /tmp/ThgE2wBlHt/view.001.rg_grp2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test047.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
- 49: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input) .. ok
+ 49: Filter -R /tmp/xlCscIPJVB/view.001.fogn (SAM input) .. ok
- 50: Count -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input) .. ok
+ 50: Count -R /tmp/xlCscIPJVB/view.001.fogn (SAM input) .. ok
- 51: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input) .. ok
+ 51: Filter -R /tmp/xlCscIPJVB/view.001.fogn (BAM input) .. ok
- 52: Count -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input) .. ok
+ 52: Count -R /tmp/xlCscIPJVB/view.001.fogn (BAM input) .. ok
- 53: Filter -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input) .. ok
+ 53: Filter -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input) .. ok
- 54: Count -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input) .. ok
+ 54: Count -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input) .. ok
- 55: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test055.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test055.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.001.sam
+ 55: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (SAM input).. ok
+ 56: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (SAM input).. ok
-.. failed ...
+ 57: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (BAM input).. ok
- 56: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (SAM input).. ok
+ 58: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (BAM input).. ok
- 57: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test057.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test057.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
+ 59: Filter -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (CRAM input).. ok
+ 60: Count -R /tmp/xlCscIPJVB/view.001.fogn -r grp2 (CRAM input).. ok
-.. failed ...
+ 61: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (SAM input).. ok
- 58: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (BAM input).. ok
+ 62: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (SAM input).. ok
- 59: Filter -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test059.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test059.sam -h -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
+ 63: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (BAM input).. ok
+ 64: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (BAM input).. ok
-.. failed ...
+ 65: Filter -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input).. ok
- 60: Count -R /tmp/ThgE2wBlHt/view.001.fogn -r grp2 (CRAM input).. ok
-
- 61: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test061.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test061.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
-
- 62: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (SAM input).. ok
-
- 63: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test063.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test063.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
-
- 64: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (BAM input).. ok
-
- 65: Filter -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test065.sam : 34 / /tmp/ThgE2wBlHt/view.001.rg_both2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test065.sam -h -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
-
- 66: Count -r grp2 -R /tmp/ThgE2wBlHt/view.001.fogn (CRAM input).. ok
+ 66: Count -r grp2 -R /tmp/xlCscIPJVB/view.001.fogn (CRAM input).. ok
Samtools-htslib-API: bam_get_library() not yet implemented
67: Filter -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test067.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.001.sam
+ /«PKGBUILDDIR»/samtools view -o /tmp/xlCscIPJVB/view.test067.sam -h -l Library 2 /tmp/xlCscIPJVB/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
68: Count -l Library 2 (SAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.001.sam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/xlCscIPJVB/view.001.sam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
69: Filter -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test069.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -o /tmp/xlCscIPJVB/view.test069.sam -h -l Library 2 /tmp/xlCscIPJVB/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
70: Count -l Library 2 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.test001.bam
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/xlCscIPJVB/view.test001.bam
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
71: Filter -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test071.sam -h -l Library 2 /tmp/ThgE2wBlHt/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -o /tmp/xlCscIPJVB/view.test071.sam -h -l Library 2 /tmp/xlCscIPJVB/view.test006.cram
.. expected failure
Samtools-htslib-API: bam_get_library() not yet implemented
72: Count -l Library 2 (CRAM input) Failed command:
- /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/ThgE2wBlHt/view.test006.cram
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/xlCscIPJVB/view.test006.cram
.. expected failure
@@ -985,153 +894,63 @@ Samtools-htslib-API: bam_get_library() not yet implemented
90: Count -q 100 (CRAM input) .. ok
- 91: Filter -x fa (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test091.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test091.sam -h -x fa /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 91: Filter -x fa (SAM input) .. ok
92: Count -x fa (SAM input) .. ok
- 93: Filter -x fa (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test093.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test093.sam -h -x fa /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 93: Filter -x fa (BAM input) .. ok
94: Count -x fa (BAM input) .. ok
- 95: Filter -x fa (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test095.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test095.sam -h -x fa /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 95: Filter -x fa (CRAM input) .. ok
96: Count -x fa (CRAM input) .. ok
- 97: Filter -x fa -x ha (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test097.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test097.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 97: Filter -x fa -x ha (SAM input) .. ok
98: Count -x fa -x ha (SAM input) .. ok
- 99: Filter -x fa -x ha (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test099.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test099.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 99: Filter -x fa -x ha (BAM input) .. ok
100: Count -x fa -x ha (BAM input) .. ok
- 101: Filter -x fa -x ha (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test101.sam : 34 / /tmp/ThgE2wBlHt/view.001.tags2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test101.sam -h -x fa -x ha /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 101: Filter -x fa -x ha (CRAM input) .. ok
102: Count -x fa -x ha (CRAM input) .. ok
- 103: Filter -x fa -r grp2 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test103.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test103.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
104: Count -x fa -r grp2 (SAM input) .. ok
- 105: Filter -x fa -r grp2 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test105.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test105.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
106: Count -x fa -r grp2 (BAM input) .. ok
- 107: Filter -x fa -r grp2 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test107.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg1.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test107.sam -h -x fa -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
108: Count -x fa -r grp2 (CRAM input) .. ok
- 109: Filter -x RG -r grp2 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test109.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test109.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
110: Count -x RG -r grp2 (SAM input) .. ok
- 111: Filter -x RG -r grp2 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test111.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test111.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
112: Count -x RG -r grp2 (BAM input) .. ok
- 113: Filter -x RG -r grp2 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test113.sam : 29 / /tmp/ThgE2wBlHt/view.001.tags_rg2.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test113.sam -h -x RG -r grp2 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
114: Count -x RG -r grp2 (CRAM input) .. ok
- 115: Filter -m 10 (SAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test115.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test115.sam -h -m 10 /tmp/ThgE2wBlHt/view.001.sam
-
-
-.. failed ...
+ 115: Filter -m 10 (SAM input) .. ok
116: Count -m 10 (SAM input) .. ok
- 117: Filter -m 10 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test117.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test117.sam -h -m 10 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 117: Filter -m 10 (BAM input) .. ok
118: Count -m 10 (BAM input) .. ok
- 119: Filter -m 10 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test119.sam : 34 / /tmp/ThgE2wBlHt/view.001.qlen10.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test119.sam -h -m 10 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 119: Filter -m 10 (CRAM input) .. ok
120: Count -m 10 (CRAM input) .. ok
@@ -1199,143 +1018,59 @@ Samtools-htslib-API: bam_get_library() not yet implemented
151: Count Z:20-40 (CRAM input) .. ok
- 152: Region ref1 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test152.sam : 34 / /tmp/ThgE2wBlHt/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test152.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1
-
-
-.. failed ...
+ 152: Region ref1 (BAM input) .. ok
153: Count ref1 (BAM input) .. ok
- 154: Region ref1 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test154.sam : 34 / /tmp/ThgE2wBlHt/view.reg1.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test154.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1
-
-
-.. failed ...
+ 154: Region ref1 (CRAM input) .. ok
155: Count ref1 (CRAM input) .. ok
- 156: Region ref1:15 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test156.sam : 31 / /tmp/ThgE2wBlHt/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test156.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15
-
-
-.. failed ...
+ 156: Region ref1:15 (BAM input) .. ok
157: Count ref1:15 (BAM input) .. ok
- 158: Region ref1:15 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test158.sam : 31 / /tmp/ThgE2wBlHt/view.reg2.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test158.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15
-
-
-.. failed ...
+ 158: Region ref1:15 (CRAM input) .. ok
159: Count ref1:15 (CRAM input) .. ok
- 160: Region ref1:15-45 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test160.sam : 31 / /tmp/ThgE2wBlHt/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test160.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 160: Region ref1:15-45 (BAM input) .. ok
161: Count ref1:15-45 (BAM input) .. ok
- 162: Region ref1:15-45 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test162.sam : 31 / /tmp/ThgE2wBlHt/view.reg3.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test162.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 162: Region ref1:15-45 (CRAM input) .. ok
163: Count ref1:15-45 (CRAM input) .. ok
- 164: Region ref1:15-45 ref2 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test164.sam : 31 / /tmp/ThgE2wBlHt/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test164.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2
-
-
-.. failed ...
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
165: Count ref1:15-45 ref2 (BAM input) .. ok
- 166: Region ref1:15-45 ref2 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test166.sam : 31 / /tmp/ThgE2wBlHt/view.reg4.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test166.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2
-
-
-.. failed ...
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
167: Count ref1:15-45 ref2 (CRAM input) .. ok
- 168: Region ref1:15-45 ref2:16 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test168.sam : 31 / /tmp/ThgE2wBlHt/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test168.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2:16
-
-
-.. failed ...
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
169: Count ref1:15-45 ref2:16 (BAM input) .. ok
- 170: Region ref1:15-45 ref2:16 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test170.sam : 31 / /tmp/ThgE2wBlHt/view.reg5.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test170.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2:16
-
-
-.. failed ...
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
- 172: Region ref1:15-45 ref2:16-31 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test172.sam : 31 / /tmp/ThgE2wBlHt/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test172.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
- 174: Region ref1:15-45 ref2:16-31 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test174.sam : 31 / /tmp/ThgE2wBlHt/view.reg6.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test174.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45 ref2:16-31
-
-
-.. failed ...
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
- 176: Region ref1:15-15 ref1:45-45 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test176.sam : 31 / /tmp/ThgE2wBlHt/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test176.sam -h /tmp/ThgE2wBlHt/view.test001.bam ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
- 178: Region ref1:15-15 ref1:45-45 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test178.sam : 31 / /tmp/ThgE2wBlHt/view.reg7.sam : 31
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test178.sam -h /tmp/ThgE2wBlHt/view.test006.cram ref1:15-15 ref1:45-45
-
-
-.. failed ...
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
@@ -1355,23 +1090,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
187: Count -q 50 ref1:15-45 (CRAM input) .. ok
- 188: Region -r grp2 ref1:15-45 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test188.sam : 28 / /tmp/ThgE2wBlHt/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test188.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test001.bam ref1:15-45
-
-
-.. failed ...
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
189: Count -r grp2 ref1:15-45 (BAM input) .. ok
- 190: Region -r grp2 ref1:15-45 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test190.sam : 28 / /tmp/ThgE2wBlHt/view.reg10.sam : 28
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test190.sam -h -r grp2 /tmp/ThgE2wBlHt/view.test006.cram ref1:15-45
-
-
-.. failed ...
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
@@ -1391,43 +1114,19 @@ Samtools-htslib-API: bam_get_library() not yet implemented
199: Count -L /«PKGBUILDDIR»/test/dat/view.002.02.bed (CRAM input).. ok
- 200: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test200.sam : 33 / /tmp/ThgE2wBlHt/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test200.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 200: 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
- 202: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test202.sam : 33 / /tmp/ThgE2wBlHt/view.bed1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test202.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 202: 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
- 204: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test204.sam : 34 / /tmp/ThgE2wBlHt/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test204.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 204: 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
- 206: Region -L /«PKGBUILDDIR»/test/dat/view.001.02.bed (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test206.sam : 34 / /tmp/ThgE2wBlHt/view.bed2.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test206.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.02.bed /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 206: 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
@@ -1463,23 +1162,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
223: 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)
- SAM files differ at /tmp/ThgE2wBlHt/view.test224.sam : 33 / /tmp/ThgE2wBlHt/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test224.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test001.bam ref1:11-16
-
-
-.. failed ...
+ 224: 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
- 226: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed ref1:11-16 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test226.sam : 33 / /tmp/ThgE2wBlHt/view.bed1r1.sam : 33
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test226.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed /tmp/ThgE2wBlHt/view.test006.cram ref1:11-16
-
-
-.. failed ...
+ 226: 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
@@ -1507,23 +1194,11 @@ Samtools-htslib-API: bam_get_library() not yet implemented
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 -q 5 (BAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test240.sam : 29 / /tmp/ThgE2wBlHt/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test240.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/ThgE2wBlHt/view.test001.bam
-
-
-.. failed ...
+ 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 -q 5 (BAM input).. ok
- 242: Region -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 (CRAM input)
- SAM files differ at /tmp/ThgE2wBlHt/view.test242.sam : 29 / /tmp/ThgE2wBlHt/view.bed1f3.sam : 29
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test242.sam -h -L /«PKGBUILDDIR»/test/dat/view.001.01.bed -q 5 /tmp/ThgE2wBlHt/view.test006.cram
-
-
-.. failed ...
+ 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 -q 5 (CRAM input).. ok
@@ -1535,141 +1210,67 @@ Samtools-htslib-API: bam_get_library() not yet implemented
247: 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
- SAM files differ at /tmp/ThgE2wBlHt/view.001.no_sq.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.001.no_sq.bam -b /tmp/ThgE2wBlHt/view.001.no_m5.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.001.no_sq.bam.sam /tmp/ThgE2wBlHt/view.001.no_sq.bam
-
-
-.. failed ...
-
- 249: Add @SQ with -t (SAM -> SAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test249.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test249.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam
-
-
-.. failed ...
-
- 250: Add @SQ with -T (SAM -> SAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test250.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test250.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam
-
-
-.. failed ...
-
- 251: Add @SQ with -t (BAM -> SAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test251.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test251.sam -h -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam
-
-
-.. failed ...
+ 248: Make BAM with no M5/UR tags .. ok
- 252: Add @SQ with -T (BAM -> SAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test252.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test252.sam -h -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
-.. failed ...
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
- 253: Add @SQ with -t (SAM -> BAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test253.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test253.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test253.bam.sam /tmp/ThgE2wBlHt/view.test253.bam
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
-.. failed ...
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
- 254: Add @SQ with -T (SAM -> BAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test254.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test254.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test254.bam.sam /tmp/ThgE2wBlHt/view.test254.bam
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
-.. failed ...
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
- 255: Add @SQ with -t (BAM -> BAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test255.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test255.bam -b -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test255.bam.sam /tmp/ThgE2wBlHt/view.test255.bam
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
-.. failed ...
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
- 256: Add @SQ with -T (BAM -> BAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test256.bam.sam : 34 / /tmp/ThgE2wBlHt/view.001.no_m5.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test256.bam -b -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test256.bam.sam /tmp/ThgE2wBlHt/view.test256.bam
+ 261: Make CRAM with no UR field .. ok
+ 262: Decoding CRAM with no UR field via -T .. ok
-.. failed ...
+ 263: CIGAR B-operator removal .. ok
- 257: Add @SQ with -t (SAM -> CRAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test257.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test257.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test257.cram.sam /tmp/ThgE2wBlHt/view.test257.cram
+ 264: Big SAM -> BAM .. ok
+ 265: Big SAM -> BAM (2 threads) .. ok
-.. failed ...
+ 266: Big SAM -> BAM (4 threads) .. ok
- 258: Add @SQ with -T (SAM -> CRAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test258.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test258.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.sam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test258.cram.sam /tmp/ThgE2wBlHt/view.test258.cram
+ 267: Big SAM -> CRAM .. ok
+ 268: Big SAM -> CRAM (2 threads) .. ok
-.. failed ...
+ 269: Big SAM -> CRAM (4 threads) .. ok
- 259: Add @SQ with -t (BAM -> CRAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test259.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test259.cram -C -t /«PKGBUILDDIR»/test/dat/view.001.fa.fai /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test259.cram.sam /tmp/ThgE2wBlHt/view.test259.cram
+ 270: Subsample 0.2 (SAM input) ............ ok
+ 271: Subsample 0.5 (SAM input) ............ ok
-.. failed ...
+ 272: Subsample 0.8 (SAM input) ............ ok
- 260: Add @SQ with -T (BAM -> CRAM)
- SAM files differ at /tmp/ThgE2wBlHt/view.test260.cram.sam : 34 / /tmp/ThgE2wBlHt/view.001.sam : 34
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/view.test260.cram -C -T /«PKGBUILDDIR»/test/dat/view.001.fa /tmp/ThgE2wBlHt/view.001.no_sq.bam && /«PKGBUILDDIR»/samtools view -h -o /tmp/ThgE2wBlHt/view.test260.cram.sam /tmp/ThgE2wBlHt/view.test260.cram
+ 273: Subsample 0.2 (BAM input) ............ ok
+ 274: Subsample 0.5 (BAM input) ............ ok
-.. failed ...
+ 275: Subsample 0.8 (BAM input) ............ ok
- 261: CIGAR B-operator removal .. ok
+ 276: Subsample 0.2 (CRAM input) ............ ok
- 262: Big SAM -> BAM .. ok
+ 277: Subsample 0.5 (CRAM input) ............ ok
- 263: Big SAM -> BAM (2 threads) .. ok
-
- 264: Big SAM -> BAM (4 threads) .. ok
-
- 265: Big SAM -> CRAM .. ok
-
- 266: Big SAM -> CRAM (2 threads) .. ok
-
- 267: Big SAM -> CRAM (4 threads) .. ok
-
- 268: Subsample 0.2 (SAM input) ............ ok
-
- 269: Subsample 0.5 (SAM input) ............ ok
-
- 270: Subsample 0.8 (SAM input) ............ ok
-
- 271: Subsample 0.2 (BAM input) ............ ok
-
- 272: Subsample 0.5 (BAM input) ............ ok
-
- 273: Subsample 0.8 (BAM input) ............ ok
-
- 274: Subsample 0.2 (CRAM input) ............ ok
-
- 275: Subsample 0.5 (CRAM input) ............ ok
-
- 276: Subsample 0.8 (CRAM input) ............ ok
+ 278: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
@@ -1697,21 +1298,10 @@ test_cat:
6: cat recompressed BAM files with new header .. ok
test_bam2fq:
- Generate BAM file
- SAM files differ at GLOB(0xc2eca0) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/bam2fq.001.bam -b /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/bam2fq.001.bam
-
-
-.. failed ...
-
- Generate CRAM file
- SAM files differ at GLOB(0xd42a60) : 45 / /«PKGBUILDDIR»/test/dat/bam2fq.001.sam : 45
- Failed command:
- /«PKGBUILDDIR»/samtools view -o /tmp/ThgE2wBlHt/bam2fq.001.cram -C /«PKGBUILDDIR»/test/dat/bam2fq.001.sam && /«PKGBUILDDIR»/samtools view -h /tmp/ThgE2wBlHt/bam2fq.001.cram
-
+ Generate BAM file .. ok
-.. failed ...
+Unsorted mode enabled
+ Generate CRAM file .. ok
[M::main_bam2fq] processed 36 reads
1: bam2fq (SAM input) .. ok
@@ -1764,28 +1354,28 @@ Samtools-htslib: fix_header() header parsing not yet implemented
Samtools-htslib: fix_header() header parsing not yet implemented
depad (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/ThgE2wBlHt/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/xlCscIPJVB/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -s (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/ThgE2wBlHt/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/xlCscIPJVB/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -u (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/ThgE2wBlHt/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/xlCscIPJVB/depad.001p.bam
.. expected failure
Samtools-htslib: fix_header() header parsing not yet implemented
depad -1 (BAM input) Failed command:
- /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/ThgE2wBlHt/depad.001p.bam
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/xlCscIPJVB/depad.001p.bam
.. expected failure
@@ -1816,16 +1406,14 @@ test_stats:
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam
-/bin/bash: line 1: 8686 Aborted ( /«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.sam /«PKGBUILDDIR»/test/dat/test_input_1_b.sam /«PKGBUILDDIR»/test/dat/test_input_1_c.sam ) 2> /tmp/BeihiK_0lz
-
-.. expected failure
+.. ok
test_merge:
/«PKGBUILDDIR»/samtools merge -s 1 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam /«PKGBUILDDIR»/test/dat/test_input_1_b.bam /«PKGBUILDDIR»/test/dat/test_input_1_c.bam
.. ok
test_merge:
- /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/ZQ1oSRFZSQ - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+ /«PKGBUILDDIR»/samtools merge -s 1 -b /tmp/t3oRPTRba5 - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
.. ok
test_fixmate:
@@ -1859,29 +1447,257 @@ test_idxstat:
Number of tests:
- total .. 342
- passed .. 237
- failed .. 87
- expected failure .. 18
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
unexpected pass .. 0
-make[2]: *** [test] Error 1
-Makefile:183: recipe for target 'test' failed
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a
+ install -d debian/samtools
+ make -j5 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/«PKGBUILDDIR»'
-dh_auto_test: make -j1 test HTSDIR=/usr/include HTSLIB=/usr/lib/mipsel-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip returned exit code 2
-make[1]: *** [override_dh_auto_test] Error 2
-debian/rules:18: recipe for target 'override_dh_auto_test' failed
make[1]: Leaving directory '/«PKGBUILDDIR»'
-make: *** [build-arch] Error 2
-debian/rules:6: recipe for target 'build-arch' failed
-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/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/mipsel-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_mipsel.deb'.
+ dpkg-genchanges -B -mmipsel Build Daemon (mipsel-aql-01) <buildd_mipsel-mipsel-aql-01 at buildd.debian.org> >../samtools_1.2-3_mipsel.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0228
+Build finished at 20150922-1635
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_mipsel.changes:
+──────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: mipsel
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: mipsel Build Daemon (mipsel-aql-01) <buildd_mipsel-mipsel-aql-01 at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ e86ec6723297d87264c9410eb8a222ffdfd1febb 372272 samtools_1.2-3_mipsel.deb
+Checksums-Sha256:
+ 321d9562ba086da596950b4f184f85d595744fc537b304a6bdcda362c6124569 372272 samtools_1.2-3_mipsel.deb
+Files:
+ 6c290d86fc238668fd7d2ec7c9438260 372272 science optional samtools_1.2-3_mipsel.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_mipsel.deb
+─────────────────────────
+
+ new debian package, version 2.0.
+ size 372272 bytes: control archive=1488 bytes.
+ 804 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: mipsel
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1126
+ Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/bin/
+-rwxr-xr-x root/root 18432 2015-09-22 16:34 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 10256 2015-09-22 16:34 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 10256 2015-09-22 16:34 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 14448 2015-09-22 16:34 ./usr/bin/md5fa
+-rwxr-xr-x root/root 10288 2015-09-22 16:34 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 873076 2015-09-22 16:34 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 22856 2015-09-22 16:34 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 16:34 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 16:34 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -1895,20 +1711,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: mipsel
-Build-Space: 21944
-Build-Time: 837
+Build-Space: 18748
+Build-Time: 736
Distribution: sid
-Fail-Stage: build
Host Architecture: mipsel
-Install-Time: 91
-Job: samtools_1.1-1
+Install-Time: 69
+Job: samtools_1.2-3
Machine Architecture: mipsel
Package: samtools
-Package-Time: 1109
-Source-Version: 1.1-1
-Space: 21944
-Status: attempted
-Version: 1.1-1
+Package-Time: 916
+Source-Version: 1.2-3
+Space: 18748
+Status: successful
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0228
-Build needed 00:18:29, 21944k disc space
+Finished at 20150922-1635
+Build needed 00:15:16, 18748k disc space
+Signature with key 'C1629605' requested:
+ signfile /home/buildd/build/samtools_1.2-3_mipsel.changes C1629605
+
+Successfully signed changes file
diff --git a/powerpc.log b/powerpc.log
deleted file mode 100644
index 97c86bd..0000000
--- a/powerpc.log
+++ /dev/null
@@ -1,899 +0,0 @@
-From buildd at praetorius.debian.org Sat Mar 30 09:16:10 2013
-Return-path: <buildd at praetorius.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1ULrtR-0002L4-GV
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:16:09 +0000
-Received: from [2001:6b0:e:2a18:214:5eff:fe97:268a]
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- CN=praetorius.debian.org,
- EMAIL=hostmaster at praetorius.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at praetorius.debian.org>)
- id 1ULrtQ-0001WL-61; Sat, 30 Mar 2013 09:16:08 +0000
-Received: from buildd by praetorius.debian.org with local (Exim 4.72)
- (envelope-from <buildd at praetorius.debian.org>)
- id 1ULrtP-0002Ne-3Z; Sat, 30 Mar 2013 09:16:07 +0000
-Date: Sat, 30 Mar 2013 09:16:07 +0000
-Message-Id: <E1ULrtP-0002Ne-3Z at praetorius.debian.org>
-From: buildd on praetorius <buildd at praetorius.debian.org>
-To: wouter at debian.org,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on powerpc (dist=sid)
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on praetorius.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (powerpc) 30 Mar 2013 09:12 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: powerpc
-Get:1 http://ftp.se.debian.org unstable InRelease [236 kB]
-Get:2 http://ftp.se.debian.org unstable/main Sources [6484 kB]
-Get:3 http://incoming.debian.org unstable InRelease [236 kB]
-Get:4 http://ftp.se.debian.org unstable/contrib Sources [51.0 kB]
-Get:5 http://ftp.se.debian.org unstable/non-free Sources [101 kB]
-Get:6 http://ftp.se.debian.org unstable/main powerpc Packages [6144 kB]
-Get:7 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:9 http://ftp.se.debian.org unstable/contrib powerpc Packages [35.8 kB]
-Get:10 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:11 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:12 http://incoming.debian.org unstable/main powerpc Packages [6144 kB]
-Get:13 http://incoming.debian.org unstable/contrib powerpc Packages [35.8 kB]
-Get:14 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:15 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:16 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:17 http://incoming.debian.org buildd-unstable/main powerpc Packages [14.0 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib powerpc Packages [14 B]
-Fetched 26.2 MB in 21s (1199 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 2s (283 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.5)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, ncurses-base, ncurses-bin, perl-base, sed, login, sysvinit-utils, sysvinit, tar, bsdutils, mount, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2-5.1)
-coreutils: already installed (8.13-3.2)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-7)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-16)
-sed: already installed (4.2.1-10)
-login: already installed (1:4.1.5.1-1)
-sysvinit-utils: already installed (2.88dsf-35)
-sysvinit: already installed (2.88dsf-35)
-tar: already installed (1.26-4)
-bsdutils: already installed (1:2.20.1-5.3)
-mount: already installed (2.20.1-5.3)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-37)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
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- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 49 not upgraded.
-Need to get 10.0 MB of archives.
-After this operation, 29.8 MB of additional disk space will be used.
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-Get:9 http://ftp.se.debian.org/debian/ unstable/main libxml2 powerpc 2.8.0+dfsg1-7+nmu1 [852 kB]
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-Get:11 http://ftp.se.debian.org/debian/ unstable/main libglib2.0-0 powerpc 2.33.12+really2.32.4-5 [1712 kB]
-Get:12 http://ftp.se.debian.org/debian/ unstable/main libcroco3 powerpc 0.6.6-2 [121 kB]
-Get:13 http://ftp.se.debian.org/debian/ unstable/main libunistring0 powerpc 0.9.3-5 [421 kB]
-Get:14 http://ftp.se.debian.org/debian/ unstable/main libgettextpo0 powerpc 0.18.1.1-10 [138 kB]
-Get:15 http://ftp.se.debian.org/debian/ unstable/main file powerpc 1:5.11-2.1 [51.7 kB]
-Get:16 http://ftp.se.debian.org/debian/ unstable/main gettext-base powerpc 0.18.1.1-10 [130 kB]
-Get:17 http://ftp.se.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp.se.debian.org/debian/ unstable/main html2text powerpc 1.3.2a-15 [105 kB]
-Get:19 http://ftp.se.debian.org/debian/ unstable/main libasprintf-dev powerpc 0.18.1.1-10 [26.9 kB]
-Get:20 http://ftp.se.debian.org/debian/ unstable/main libgettextpo-dev powerpc 0.18.1.1-10 [184 kB]
-Get:21 http://ftp.se.debian.org/debian/ unstable/main gettext powerpc 0.18.1.1-10 [1766 kB]
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-Get:24 http://ftp.se.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.se.debian.org/debian/ unstable/main diffstat powerpc 1.55-3 [29.2 kB]
-Get:26 http://ftp.se.debian.org/debian/ unstable/main libtinfo-dev powerpc 5.9-10 [105 kB]
-Get:27 http://ftp.se.debian.org/debian/ unstable/main libncurses5-dev powerpc 5.9-10 [211 kB]
-Get:28 http://ftp.se.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp.se.debian.org/debian/ unstable/main zlib1g-dev powerpc 1:1.2.7.dfsg-13 [213 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.0 MB in 1s (5075 kB/s)
-Selecting previously unselected package libpipeline1:powerpc.
-(Reading database ... 10827 files and directories currently installed.)
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-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_powerpc.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:powerpc.
-Unpacking libasprintf0c2:powerpc (from .../libasprintf0c2_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package libmagic1:powerpc.
-Unpacking libmagic1:powerpc (from .../libmagic1_1%3a5.11-2.1_powerpc.deb) ...
-Selecting previously unselected package libpcre3:powerpc.
-Unpacking libpcre3:powerpc (from .../libpcre3_1%3a8.31-2_powerpc.deb) ...
-Selecting previously unselected package libxml2:powerpc.
-Unpacking libxml2:powerpc (from .../libxml2_2.8.0+dfsg1-7+nmu1_powerpc.deb) ...
-Selecting previously unselected package libffi5:powerpc.
-Unpacking libffi5:powerpc (from .../libffi5_3.0.10-3_powerpc.deb) ...
-Selecting previously unselected package libglib2.0-0:powerpc.
-Unpacking libglib2.0-0:powerpc (from .../libglib2.0-0_2.33.12+really2.32.4-5_powerpc.deb) ...
-Selecting previously unselected package libcroco3:powerpc.
-Unpacking libcroco3:powerpc (from .../libcroco3_0.6.6-2_powerpc.deb) ...
-Selecting previously unselected package libunistring0:powerpc.
-Unpacking libunistring0:powerpc (from .../libunistring0_0.9.3-5_powerpc.deb) ...
-Selecting previously unselected package libgettextpo0:powerpc.
-Unpacking libgettextpo0:powerpc (from .../libgettextpo0_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_powerpc.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_powerpc.deb) ...
-Selecting previously unselected package libasprintf-dev:powerpc.
-Unpacking libasprintf-dev:powerpc (from .../libasprintf-dev_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package libgettextpo-dev:powerpc.
-Unpacking libgettextpo-dev:powerpc (from .../libgettextpo-dev_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_powerpc.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_powerpc.deb) ...
-Selecting previously unselected package libtinfo-dev:powerpc.
-Unpacking libtinfo-dev:powerpc (from .../libtinfo-dev_5.9-10_powerpc.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_powerpc.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:powerpc.
-Unpacking zlib1g-dev:powerpc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_powerpc.deb) ...
-Setting up libpipeline1:powerpc (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:powerpc (0.18.1.1-10) ...
-Setting up libmagic1:powerpc (1:5.11-2.1) ...
-Setting up libpcre3:powerpc (1:8.31-2) ...
-Setting up libxml2:powerpc (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:powerpc (3.0.10-3) ...
-Setting up libglib2.0-0:powerpc (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:powerpc (0.6.6-2) ...
-Setting up libunistring0:powerpc (0.9.3-5) ...
-Setting up libgettextpo0:powerpc (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:powerpc (0.18.1.1-10) ...
-Setting up libgettextpo-dev:powerpc (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:powerpc (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:powerpc (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 49 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-powerpc64 powerpc (ppc64)
-Toolchain package versions: binutils_2.22-7.1 dpkg-dev_1.16.9 g++-4.6_4.6.3-14 gcc-4.6_4.6.3-14 libc6-dev_2.13-37 libstdc++6_4.7.2-4 libstdc++6-4.6-dev_4.6.3-14 linux-libc-dev_3.2.35-2
-Package versions: apt_0.9.7.7 base-files_7.1 base-passwd_3.5.26 bash_4.2-5.1 bash-completion_1:2.0-1 binutils_2.22-7.1 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.5 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14 dash_0.5.7-3 debconf_1.5.48 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-7 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 fi [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture powerpc
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-powerpc-fWt5pF/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_powerpc.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_powerpc.deb'.
- dpkg-genchanges -B -mpowerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org> >../samtools_0.1.19-1_powerpc.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0916
-
-samtools_0.1.19-1_powerpc.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: powerpc
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: powerpc Build Daemon (praetorius) <buildd_powerpc-praetorius at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- bc79b2d19863315cae32a48cdf70c20ba475e82c 536000 samtools_0.1.19-1_powerpc.deb
- 0faf6c3cec234f37a77e07ced7bbfe098d26f957 116042 libbam-dev_0.1.19-1_powerpc.deb
-Checksums-Sha256:
- aae2820e92c0f383e1a5f47e380d8961cc415d93326d0d628d8e0740f2115ace 536000 samtools_0.1.19-1_powerpc.deb
- 247e56f8c2ce2d645706ce2b775d50c83fe61e4986943f1c5748310d1baa924a 116042 libbam-dev_0.1.19-1_powerpc.deb
-Files:
- 11edcf731d65e17ea5527d9acd7f5334 536000 science optional samtools_0.1.19-1_powerpc.deb
- 26e39ba519db79a253337b6d9fe4c237 116042 libdevel optional libbam-dev_0.1.19-1_powerpc.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_powerpc.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 536000 bytes: control archive= 1931 bytes.
- 32 bytes, 1 lines conffiles
- 794 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1319
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:15 ./
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/bin/
--rwxr-xr-x root/root 153760 2013-03-30 09:15 ./usr/bin/bcftools
--rwxr-xr-x root/root 26228 2013-03-30 09:15 ./usr/bin/razip
--rwxr-xr-x root/root 419208 2013-03-30 09:15 ./usr/bin/samtools
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/samtools/
--rwxr-xr-x root/root 175244 2013-03-30 09:15 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 17908 2013-03-30 09:15 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 9700 2013-03-30 09:15 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 13796 2013-03-30 09:15 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 22064 2013-03-30 09:15 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 9700 2013-03-30 09:15 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9672 2013-03-30 09:15 ./usr/lib/samtools/md5sum-lite
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/man/man1/
--rw-r--r-- root/root 10654 2013-03-30 09:15 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2013-03-30 09:15 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:15 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 1966 2013-03-30 09:15 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/samtools/
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:15 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:15 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_powerpc.deb
-───────────────────────────────
-
- new debian package, version 2.0.
- size 116042 bytes: control archive= 926 bytes.
- 714 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: powerpc
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 385
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/lib/
--rw-r--r-- root/root 271770 2013-03-30 09:15 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/include/samtools/
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:15 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-powerpc-sbuild-4da4802a-fbb1-47e3-b713-2d08e5d84ffc/build/buildd-samtools_0.1.19-1-powerpc-fWt5pF
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: powerpc
-Build-Space: 12352
-Build-Time: 88
-Distribution: sid
-Install-Time: 57
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 184
-Source-Version: 0.1.19-1
-Space: 12352
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0916
-Build needed 00:03:04, 12352k disc space
-Signature with key '0E6E7223' requested:
-
diff --git a/ppc64el.log b/ppc64el.log
index a52ee78..e024443 100644
--- a/ppc64el.log
+++ b/ppc64el.log
@@ -1,68 +1,45 @@
-From buildd at ppc64el2.debian.net Thu Sep 25 02:55:34 2014
-Return-path: <buildd at ppc64el2.debian.net>
-Received: from hall.aurel32.net ([2001:bc8:30d7:101::1])
- by wuiet.debian.org with esmtps (TLS1.2:DHE_RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at ppc64el2.debian.net>)
- id 1XWzDS-0001tF-Li
- for logs at buildd.debian.org; Thu, 25 Sep 2014 02:55:34 +0000
-Received: from [91.121.150.236] (helo=ppc64el2.debian.net)
- by hall.aurel32.net with esmtps (TLS1.2:RSA_AES_128_CBC_SHA1:128)
- (Exim 4.80) (envelope-from <buildd at ppc64el2.debian.net>)
- id 1XWzDR-0005pK-3P; Thu, 25 Sep 2014 04:55:33 +0200
-Received: from buildd by ppc64el2.debian.net with local (Exim 4.84)
- (envelope-from <buildd at ppc64el2.debian.net>)
- id 1XWzDH-0001M0-Oc; Thu, 25 Sep 2014 04:55:23 +0200
-Content-Transfer-Encoding: binary
-MIME-Version: 1.0
-X-Mailer: MIME::Lite 3.030 (F2.85; T2.06; A2.13; B3.14; Q3.13)
-Date: Thu, 25 Sep 2014 04:55:23 +0200
-From: buildd on ppc64el2 <buildd at ppc64el2.debian.net>
-To: buildd-porters at ppc64el2.debian.net,builddlogs at aurel32.net
-Subject: Log for attempted build of samtools_1.1-1 on ppc64el (dist=sid)
-Message-Id: <E1XWzDH-0001M0-Oc at ppc64el2.debian.net>
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.64.0 (17 May 2013) on ppc64el2.debian.net
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on ppc64el-osuosl-01.debian.org
╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 1.1-1 (ppc64el) 25 Sep 2014 02:24 ║
+║ samtools 1.2-3 (ppc64el) 22 Sep 2015 16:10 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
-Version: 1.1-1
-Source Version: 1.1-1
+Version: 1.2-3
+Source Version: 1.2-3
Distribution: sid
Machine Architecture: ppc64el
Host Architecture: ppc64el
Build Architecture: ppc64el
-I: NOTICE: Log filtering will replace 'build/samtools-tWy_2r/samtools-1.1' with '«PKGBUILDDIR»'
-I: NOTICE: Log filtering will replace 'build/samtools-tWy_2r' with '«BUILDDIR»'
-I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-a0d75f02-8cc1-4fe2-b92b-11ac6d034834' with '«CHROOT»'
+I: NOTICE: Log filtering will replace 'build/samtools-WcsdPk/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-WcsdPk' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-ppc64el-sbuild-4b9bc1a9-86e5-4c4f-bcc5-94dabfd7ad61' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
-Get:1 http://ftp.debian.org unstable InRelease [233 kB]
-Get:2 http://incoming.debian.org buildd-unstable InRelease [110 kB]
-Get:3 http://incoming.debian.org buildd-unstable/main Sources [358 kB]
-Get:4 http://ftp.debian.org unstable/main Sources [7548 kB]
-Get:5 http://incoming.debian.org buildd-unstable/contrib Sources [1136 B]
-Get:6 http://incoming.debian.org buildd-unstable/non-free Sources [1664 B]
-Get:7 http://incoming.debian.org buildd-unstable/main ppc64el Packages [273 kB]
-Get:8 http://incoming.debian.org buildd-unstable/contrib ppc64el Packages [844 B]
-Get:9 http://ftp.debian.org unstable/contrib Sources [57.1 kB]
-Get:10 http://ftp.debian.org unstable/non-free Sources [107 kB]
-Get:11 http://ftp.debian.org unstable/main ppc64el Packages [6538 kB]
-Get:12 http://ftp.debian.org unstable/contrib ppc64el Packages [38.3 kB]
-Get:13 http://ftp.fr.debian.org unstable InRelease [233 kB]
-Get:14 http://ftp.fr.debian.org unstable/main Sources [7548 kB]
-Get:15 http://ftp.fr.debian.org unstable/contrib Sources [57.1 kB]
-Get:16 http://ftp.fr.debian.org unstable/non-free Sources [107 kB]
-Get:17 http://ftp.fr.debian.org unstable/main ppc64el Packages [6538 kB]
-Get:18 http://ftp.fr.debian.org unstable/contrib ppc64el Packages [38.3 kB]
-Fetched 29.8 MB in 5s (5242 kB/s)
+Get:1 http://debian.osuosl.org unstable InRelease [253 kB]
+Get:2 http://debian.osuosl.org unstable/main Sources [8093 kB]
+Get:3 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:4 http://ftp.debian.org unstable InRelease [253 kB]
+Get:5 http://debian.osuosl.org unstable/contrib Sources [59.7 kB]
+Get:6 http://debian.osuosl.org unstable/non-free Sources [106 kB]
+Get:7 http://debian.osuosl.org unstable/main ppc64el Packages [7286 kB]
+Get:8 http://incoming.debian.org buildd-unstable/main Sources [341 kB]
+Get:9 http://debian.osuosl.org unstable/contrib ppc64el Packages [42.7 kB]
+Get:10 http://ftp.debian.org unstable/main Sources [8093 kB]
+Get:11 http://incoming.debian.org buildd-unstable/contrib Sources [1428 B]
+Get:12 http://incoming.debian.org buildd-unstable/non-free Sources [32 B]
+Get:13 http://incoming.debian.org buildd-unstable/main ppc64el Packages [97.8 kB]
+Get:14 http://incoming.debian.org buildd-unstable/contrib ppc64el Packages [1060 B]
+Get:15 http://ftp.debian.org unstable/contrib Sources [59.7 kB]
+Get:16 http://ftp.debian.org unstable/non-free Sources [106 kB]
+Get:17 http://ftp.debian.org unstable/main ppc64el Packages [7286 kB]
+Get:18 http://ftp.debian.org unstable/contrib ppc64el Packages [42.7 kB]
+Fetched 32.2 MB in 7s (4218 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -83,20 +60,30 @@ Building dependency tree...
Reading state information...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
-Need to get 4333 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (dsc) [2104 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (tar) [4321 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.1-1 (diff) [10.2 kB]
-Fetched 4333 kB in 0s (6428 kB/s)
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 2s (1872 kB/s)
Download complete and in download only mode
-Check arch
-──────────
+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-CckoiP/apt_archive/sbuild-build-depends-core-dummy.deb'.
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-NwlZLO/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -110,18 +97,22 @@ Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
-0 upgraded, 1 newly installed, 0 to remove and 10 not upgraded.
-Need to get 0 B/820 B of archives.
+0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
+Need to get 0 B/772 B of archives.
After this operation, 0 B of additional disk space will be used.
-Selecting previously unselected package sbuild-build-depends-core-dummy.
-(Reading database ... 11706 files and directories currently installed.)
-Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
-Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
-Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
-Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.9.1), g++ (>= 4:4.9.1), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libncurses5-dev, libhts-dev (>= 1.0), zlib1g-dev, tabix (>= 1.0)
-dpkg-deb: building package `sbuild-build-depends-samtools-dummy' in `/«BUILDDIR»/resolver-4i5qbP/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11740 files and directories currently installed.)
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-HBCtap/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Reading package lists...
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
@@ -134,170 +125,170 @@ Building dependency tree...
Reading state information...
The following extra packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sysvinit tabix zlib1g-dev
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
Suggested packages:
- wamerican wordlist whois vacation dh-make gettext-doc groff ncurses-doc less
- www-browser libmail-box-perl
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
Recommended packages:
- curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
- libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
- intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0 libhts-dev
- libhts1 libmagic1 libncurses5-dev libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy sysvinit tabix
- zlib1g-dev
-0 upgraded, 26 newly installed, 0 to remove and 10 not upgraded.
-Need to get 9950 kB/9951 kB of archives.
-After this operation, 31.9 MB of additional disk space will be used.
-Get:1 http://ftp.fr.debian.org/debian/ unstable/main libpipeline1 ppc64el 1.3.1-1 [25.0 kB]
-Get:2 http://ftp.fr.debian.org/debian/ unstable/main groff-base ppc64el 1.22.2-8 [1216 kB]
-Get:3 http://ftp.fr.debian.org/debian/ unstable/main bsdmainutils ppc64el 9.0.5+b1 [180 kB]
-Get:4 http://ftp.fr.debian.org/debian/ unstable/main man-db ppc64el 2.7.0.1-1 [980 kB]
-Get:5 http://ftp.fr.debian.org/debian/ unstable/main bash-completion all 1:2.1-4 [182 kB]
-Get:6 http://ftp.fr.debian.org/debian/ unstable/main libasprintf0c2 ppc64el 0.19.2-2 [30.9 kB]
-Get:7 http://ftp.fr.debian.org/debian/ unstable/main libmagic1 ppc64el 1:5.19-2+b1 [235 kB]
-Get:8 http://ftp.fr.debian.org/debian/ unstable/main libxml2 ppc64el 2.9.1+dfsg1-4+b1 [731 kB]
-Get:9 http://ftp.fr.debian.org/debian/ unstable/main libffi6 ppc64el 3.1-2+b1 [20.4 kB]
-Get:10 http://ftp.fr.debian.org/debian/ unstable/main libglib2.0-0 ppc64el 2.42.0-1 [2360 kB]
-Get:11 http://ftp.fr.debian.org/debian/ unstable/main libcroco3 ppc64el 0.6.8-3+b1 [125 kB]
-Get:12 http://ftp.fr.debian.org/debian/ unstable/main libhts1 ppc64el 1.1-1 [192 kB]
-Get:13 http://ftp.fr.debian.org/debian/ unstable/main libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
-Get:14 http://ftp.fr.debian.org/debian/ unstable/main sysvinit ppc64el 2.88dsf-53.4 [98.5 kB]
-Get:15 http://ftp.fr.debian.org/debian/ unstable/main file ppc64el 1:5.19-2+b1 [58.5 kB]
-Get:16 http://ftp.fr.debian.org/debian/ unstable/main gettext-base ppc64el 0.19.2-2 [118 kB]
-Get:17 http://ftp.fr.debian.org/debian/ unstable/main gettext ppc64el 0.19.2-2 [1190 kB]
-Get:18 http://ftp.fr.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:19 http://ftp.fr.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu3 [220 kB]
-Get:20 http://ftp.fr.debian.org/debian/ unstable/main debhelper all 9.20140817 [814 kB]
-Get:21 http://ftp.fr.debian.org/debian/ unstable/main libhts-dev ppc64el 1.1-1 [246 kB]
-Get:22 http://ftp.fr.debian.org/debian/ unstable/main libtinfo-dev ppc64el 5.9+20140913-1 [77.9 kB]
-Get:23 http://ftp.fr.debian.org/debian/ unstable/main libncurses5-dev ppc64el 5.9+20140913-1 [175 kB]
-Get:24 http://ftp.fr.debian.org/debian/ unstable/main tabix ppc64el 1.1-1 [174 kB]
-Get:25 http://ftp.fr.debian.org/debian/ unstable/main zlib1g-dev ppc64el 1:1.2.8.dfsg-2+b1 [206 kB]
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 8 not upgraded.
+Need to get 17.9 MB/17.9 MB of archives.
+After this operation, 69.6 MB of additional disk space will be used.
+Get:1 http://debian.osuosl.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://debian.osuosl.org/debian/ unstable/main groff-base ppc64el 1.22.3-1 [1237 kB]
+Get:3 http://debian.osuosl.org/debian/ unstable/main bsdmainutils ppc64el 9.0.6 [181 kB]
+Get:4 http://debian.osuosl.org/debian/ unstable/main libpipeline1 ppc64el 1.4.1-1 [26.4 kB]
+Get:5 http://debian.osuosl.org/debian/ unstable/main man-db ppc64el 2.7.3-1 [984 kB]
+Get:6 http://debian.osuosl.org/debian/ unstable/main libffi6 ppc64el 3.2.1-3 [20.4 kB]
+Get:7 http://debian.osuosl.org/debian/ unstable/main libglib2.0-0 ppc64el 2.44.1-1.1 [2334 kB]
+Get:8 http://debian.osuosl.org/debian/ unstable/main libicu55 ppc64el 55.1-5 [7624 kB]
+Get:9 http://debian.osuosl.org/debian/ unstable/main libxml2 ppc64el 2.9.2+zdfsg1-4 [827 kB]
+Get:10 http://debian.osuosl.org/debian/ unstable/main libcroco3 ppc64el 0.6.8-3+b1 [125 kB]
+Get:11 http://debian.osuosl.org/debian/ unstable/main libunistring0 ppc64el 0.9.3-5.2+b1 [263 kB]
+Get:12 http://debian.osuosl.org/debian/ unstable/main libmagic1 ppc64el 1:5.25-1 [253 kB]
+Get:13 http://debian.osuosl.org/debian/ unstable/main file ppc64el 1:5.25-1 [61.6 kB]
+Get:14 http://debian.osuosl.org/debian/ unstable/main gettext-base ppc64el 0.19.6-1 [121 kB]
+Get:15 http://debian.osuosl.org/debian/ unstable/main gettext ppc64el 0.19.6-1 [1418 kB]
+Get:16 http://debian.osuosl.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://debian.osuosl.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://debian.osuosl.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://debian.osuosl.org/debian/ unstable/main libhts1 ppc64el 1.2.1-1 [216 kB]
+Get:20 http://debian.osuosl.org/debian/ unstable/main libhts-dev ppc64el 1.2.1-1 [274 kB]
+Get:21 http://debian.osuosl.org/debian/ unstable/main libio-pty-perl ppc64el 1:1.08-1 [35.0 kB]
+Get:22 http://debian.osuosl.org/debian/ unstable/main libtinfo-dev ppc64el 6.0+20150810-1 [77.8 kB]
+Get:23 http://debian.osuosl.org/debian/ unstable/main libncurses5-dev ppc64el 6.0+20150810-1 [172 kB]
+Get:24 http://debian.osuosl.org/debian/ unstable/main tabix ppc64el 1.2.1-1 [206 kB]
+Get:25 http://debian.osuosl.org/debian/ unstable/main zlib1g-dev ppc64el 1:1.2.8.dfsg-2+b1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9950 kB in 3s (2767 kB/s)
-Selecting previously unselected package libpipeline1:ppc64el.
-(Reading database ... 11706 files and directories currently installed.)
-Preparing to unpack .../libpipeline1_1.3.1-1_ppc64el.deb ...
-Unpacking libpipeline1:ppc64el (1.3.1-1) ...
-Selecting previously unselected package groff-base.
-Preparing to unpack .../groff-base_1.22.2-8_ppc64el.deb ...
-Unpacking groff-base (1.22.2-8) ...
-Selecting previously unselected package bsdmainutils.
-Preparing to unpack .../bsdmainutils_9.0.5+b1_ppc64el.deb ...
-Unpacking bsdmainutils (9.0.5+b1) ...
-Selecting previously unselected package man-db.
-Preparing to unpack .../man-db_2.7.0.1-1_ppc64el.deb ...
-Unpacking man-db (2.7.0.1-1) ...
-Selecting previously unselected package bash-completion.
-Preparing to unpack .../bash-completion_1%3a2.1-4_all.deb ...
-Unpacking bash-completion (1:2.1-4) ...
-Selecting previously unselected package libasprintf0c2:ppc64el.
-Preparing to unpack .../libasprintf0c2_0.19.2-2_ppc64el.deb ...
-Unpacking libasprintf0c2:ppc64el (0.19.2-2) ...
-Selecting previously unselected package libmagic1:ppc64el.
-Preparing to unpack .../libmagic1_1%3a5.19-2+b1_ppc64el.deb ...
-Unpacking libmagic1:ppc64el (1:5.19-2+b1) ...
-Selecting previously unselected package libxml2:ppc64el.
-Preparing to unpack .../libxml2_2.9.1+dfsg1-4+b1_ppc64el.deb ...
-Unpacking libxml2:ppc64el (2.9.1+dfsg1-4+b1) ...
-Selecting previously unselected package libffi6:ppc64el.
-Preparing to unpack .../libffi6_3.1-2+b1_ppc64el.deb ...
-Unpacking libffi6:ppc64el (3.1-2+b1) ...
-Selecting previously unselected package libglib2.0-0:ppc64el.
-Preparing to unpack .../libglib2.0-0_2.42.0-1_ppc64el.deb ...
-Unpacking libglib2.0-0:ppc64el (2.42.0-1) ...
-Selecting previously unselected package libcroco3:ppc64el.
-Preparing to unpack .../libcroco3_0.6.8-3+b1_ppc64el.deb ...
-Unpacking libcroco3:ppc64el (0.6.8-3+b1) ...
-Selecting previously unselected package libhts1:ppc64el.
-Preparing to unpack .../libhts1_1.1-1_ppc64el.deb ...
-Unpacking libhts1:ppc64el (1.1-1) ...
-Selecting previously unselected package libunistring0:ppc64el.
-Preparing to unpack .../libunistring0_0.9.3-5.2+b1_ppc64el.deb ...
-Unpacking libunistring0:ppc64el (0.9.3-5.2+b1) ...
-Selecting previously unselected package sysvinit.
-Preparing to unpack .../sysvinit_2.88dsf-53.4_ppc64el.deb ...
-Unpacking sysvinit (2.88dsf-53.4) ...
-Selecting previously unselected package file.
-Preparing to unpack .../file_1%3a5.19-2+b1_ppc64el.deb ...
-Unpacking file (1:5.19-2+b1) ...
-Selecting previously unselected package gettext-base.
-Preparing to unpack .../gettext-base_0.19.2-2_ppc64el.deb ...
-Unpacking gettext-base (0.19.2-2) ...
-Selecting previously unselected package gettext.
-Preparing to unpack .../gettext_0.19.2-2_ppc64el.deb ...
-Unpacking gettext (0.19.2-2) ...
-Selecting previously unselected package intltool-debian.
-Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
-Unpacking intltool-debian (0.35.0+20060710.1) ...
-Selecting previously unselected package po-debconf.
-Preparing to unpack .../po-debconf_1.0.16+nmu3_all.deb ...
-Unpacking po-debconf (1.0.16+nmu3) ...
-Selecting previously unselected package debhelper.
-Preparing to unpack .../debhelper_9.20140817_all.deb ...
-Unpacking debhelper (9.20140817) ...
-Selecting previously unselected package libhts-dev:ppc64el.
-Preparing to unpack .../libhts-dev_1.1-1_ppc64el.deb ...
-Unpacking libhts-dev:ppc64el (1.1-1) ...
-Selecting previously unselected package libtinfo-dev:ppc64el.
-Preparing to unpack .../libtinfo-dev_5.9+20140913-1_ppc64el.deb ...
-Unpacking libtinfo-dev:ppc64el (5.9+20140913-1) ...
-Selecting previously unselected package libncurses5-dev:ppc64el.
-Preparing to unpack .../libncurses5-dev_5.9+20140913-1_ppc64el.deb ...
-Unpacking libncurses5-dev:ppc64el (5.9+20140913-1) ...
-Selecting previously unselected package tabix.
-Preparing to unpack .../tabix_1.1-1_ppc64el.deb ...
-Unpacking tabix (1.1-1) ...
-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.
-Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
-Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Setting up libpipeline1:ppc64el (1.3.1-1) ...
-Setting up groff-base (1.22.2-8) ...
-Setting up bsdmainutils (9.0.5+b1) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.7.0.1-1) ...
-Not building database; man-db/auto-update is not 'true'.
-Setting up bash-completion (1:2.1-4) ...
-Setting up libasprintf0c2:ppc64el (0.19.2-2) ...
-Setting up libmagic1:ppc64el (1:5.19-2+b1) ...
-Setting up libxml2:ppc64el (2.9.1+dfsg1-4+b1) ...
-Setting up libffi6:ppc64el (3.1-2+b1) ...
-Setting up libglib2.0-0:ppc64el (2.42.0-1) ...
-No schema files found: doing nothing.
-Setting up libcroco3:ppc64el (0.6.8-3+b1) ...
-Setting up libhts1:ppc64el (1.1-1) ...
-Setting up libunistring0:ppc64el (0.9.3-5.2+b1) ...
-Setting up sysvinit (2.88dsf-53.4) ...
-Setting up file (1:5.19-2+b1) ...
-Setting up gettext-base (0.19.2-2) ...
-Setting up gettext (0.19.2-2) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu3) ...
-Setting up debhelper (9.20140817) ...
-Setting up libhts-dev:ppc64el (1.1-1) ...
-Setting up libtinfo-dev:ppc64el (5.9+20140913-1) ...
-Setting up libncurses5-dev:ppc64el (5.9+20140913-1) ...
-Setting up tabix (1.1-1) ...
-Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
-Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
-Processing triggers for libc-bin (2.19-11) ...
+Fetched 17.9 MB in 0s (26.1 MB/s)
+Selecting previously unselected package bash-completion.
+(Reading database ...
(Reading database ... 5%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 11740 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_ppc64el.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_ppc64el.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:ppc64el.
+Preparing to unpack .../libpipeline1_1.4.1-1_ppc64el.deb ...
+Unpacking libpipeline1:ppc64el (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_ppc64el.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:ppc64el.
+Preparing to unpack .../libffi6_3.2.1-3_ppc64el.deb ...
+Unpacking libffi6:ppc64el (3.2.1-3) ...
+Selecting previously unselected package libglib2.0-0:ppc64el.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_ppc64el.deb ...
+Unpacking libglib2.0-0:ppc64el (2.44.1-1.1) ...
+Selecting previously unselected package libicu55:ppc64el.
+Preparing to unpack .../libicu55_55.1-5_ppc64el.deb ...
+Unpacking libicu55:ppc64el (55.1-5) ...
+Selecting previously unselected package libxml2:ppc64el.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_ppc64el.deb ...
+Unpacking libxml2:ppc64el (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libcroco3:ppc64el.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_ppc64el.deb ...
+Unpacking libcroco3:ppc64el (0.6.8-3+b1) ...
+Selecting previously unselected package libunistring0:ppc64el.
+Preparing to unpack .../libunistring0_0.9.3-5.2+b1_ppc64el.deb ...
+Unpacking libunistring0:ppc64el (0.9.3-5.2+b1) ...
+Selecting previously unselected package libmagic1:ppc64el.
+Preparing to unpack .../libmagic1_1%3a5.25-1_ppc64el.deb ...
+Unpacking libmagic1:ppc64el (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_ppc64el.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_ppc64el.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_ppc64el.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:ppc64el.
+Preparing to unpack .../libhts1_1.2.1-1_ppc64el.deb ...
+Unpacking libhts1:ppc64el (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:ppc64el.
+Preparing to unpack .../libhts-dev_1.2.1-1_ppc64el.deb ...
+Unpacking libhts-dev:ppc64el (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1_ppc64el.deb ...
+Unpacking libio-pty-perl (1:1.08-1) ...
+Selecting previously unselected package libtinfo-dev:ppc64el.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_ppc64el.deb ...
+Unpacking libtinfo-dev:ppc64el (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:ppc64el.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_ppc64el.deb ...
+Unpacking libncurses5-dev:ppc64el (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../tabix_1.2.1-1_ppc64el.deb ...
+Unpacking tabix (1.2.1-1) ...
+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.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:ppc64el (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:ppc64el (3.2.1-3) ...
+Setting up libglib2.0-0:ppc64el (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libicu55:ppc64el (55.1-5) ...
+Setting up libxml2:ppc64el (2.9.2+zdfsg1-4) ...
+Setting up libcroco3:ppc64el (0.6.8-3+b1) ...
+Setting up libunistring0:ppc64el (0.9.3-5.2+b1) ...
+Setting up libmagic1:ppc64el (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:ppc64el (1.2.1-1) ...
+Setting up libhts-dev:ppc64el (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1) ...
+Setting up libtinfo-dev:ppc64el (6.0+20150810-1) ...
+Setting up libncurses5-dev:ppc64el (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:ppc64el (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
-Kernel: Linux 3.16-1-powerpc64le ppc64el (ppc64le)
-Toolchain package versions: binutils_2.24.51.20140918-1 dpkg-dev_1.17.13 g++-4.9_4.9.1-15 gcc-4.9_4.9.1-15 libc6-dev_2.19-11 libstdc++-4.9-dev_4.9.1-15 libstdc++6_4.9.1-15 linux-libc-dev_3.16.3-1
-Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.0.9.1 base-files_7.5+b1 base-passwd_3.5.36 bash_4.3-9 bash-completion_1:2.1-4 binutils_2.24.51.20140918-1 bsdmainutils_9.0.5+b1 bsdutils_1:2.20.1-5.8+b1 build-essential_11.7+b1 bzip2_1.0.6-7+b1 coreutils_8.23-2 cpp_4:4.9.1-4 cpp-4.9_4.9.1-15 dash_0.5.7-4+b1 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-2+b1 debhelper_9.20140817 debian-archive-keyring_2014.1 debianutils_4.4+b1 diffutils_1:3.3-1+b1 dmsetup_2:1.02.90-1 dpkg_1.17.13 [...]
+Kernel: Linux 3.16.0-4-powerpc64le ppc64el (ppc64le)
+Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-5_5.2.1-17 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-3 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-5_5.2.1-17 dash_0.5.7-4+b2 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1+b2 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 faker [...]
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
@@ -308,16 +299,15 @@ Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Thu Sep 25 00:09:33 2014 UTC using RSA key ID 2295D502
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_1.1-1.dsc
-dpkg-source: info: extracting samtools in samtools-1.1
-dpkg-source: info: unpacking samtools_1.1.orig.tar.gz
-dpkg-source: info: unpacking samtools_1.1-1.debian.tar.xz
-dpkg-source: info: applying fix_coverage_cap.patch
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
-dpkg-source: info: applying debian-changes
+dpkg-source: info: applying i386-build.patch
Check disc space
────────────────
@@ -327,17 +317,17 @@ Sufficient free space for build
User Environment
────────────────
-DEB_BUILD_OPTIONS=parallel=8
+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-ppc64el-sbuild
SCHROOT_CHROOT_NAME=sid-ppc64el-sbuild
SCHROOT_COMMAND=env
-SCHROOT_GID=1002
+SCHROOT_GID=1009
SCHROOT_GROUP=buildd
-SCHROOT_SESSION_ID=sid-ppc64el-sbuild-a0d75f02-8cc1-4fe2-b92b-11ac6d034834
-SCHROOT_UID=1002
+SCHROOT_SESSION_ID=sid-ppc64el-sbuild-4b9bc1a9-86e5-4c4f-bcc5-94dabfd7ad61
+SCHROOT_UID=2952
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
@@ -346,16 +336,16 @@ dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 1.1-1
+dpkg-buildpackage: source version 1.2-3
dpkg-buildpackage: source distribution unstable
- dpkg-source --before-build samtools-1.1
+ dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture ppc64el
-dpkg-source: info: using options from samtools-1.1/debian/source/options: --single-debian-patch
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
- make -j8 distclean
+ make -j4 distclean
make[1]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
@@ -370,9 +360,11 @@ make[1]: Leaving directory '/«PKGBUILDDIR»'
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 . \( \( -type f -a \
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
@@ -393,7 +385,7 @@ dh_auto_build -- \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
LDLIBS="-lhts"
- make -j8 HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+ make -j4 HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
make[2]: Entering directory '/«PKGBUILDDIR»'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
@@ -409,8 +401,7 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
-echo '#define SAMTOOLS_VERSION "1.1"' > version.h
-gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kaln.o kaln.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
@@ -455,22 +446,23 @@ gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFF
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -l [...]
gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lcurses [...]
gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
-gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/powerpc64le-linux-gnu/libhts.a -lhts -lz
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
debian/rules override_dh_auto_test
@@ -479,41 +471,1232 @@ dh_auto_test -- \
HTSDIR="/usr/include" \
HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a \
BGZIP=/usr/bin/bgzip
- make -j8 test HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
+ make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/«PKGBUILDDIR»'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
-/usr/bin/bgzip -c -b 65272 -s 5 /tmp/OsbUKpLXsb/bgzip.dat.gz
+/usr/bin/bgzip -c -b 65272 -s 5 /tmp/V45HaBNwUA/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 979200 -s 6 /tmp/V45HaBNwUA/bgzip.dat.gz
+.. ok
+
+/usr/bin/bgzip -c -b 652804 -s 6 /tmp/V45HaBNwUA/bgzip.dat.gz
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 3:11-13 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 2:998-1003 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 1:100-104 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa 1:99998-100007 | grep -v '^>'
+.. ok
+
+/«PKGBUILDDIR»/samtools faidx /tmp/V45HaBNwUA/faidx.fa.gz 1:99998-100007 | grep -v '^>'
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools index /tmp/V45HaBNwUA/large_chrom.bam
+
+.. expected failure
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/V45HaBNwUA/large_chrom.bam ref2
+.. ok
+
+test_index:
+ /«PKGBUILDDIR»/samtools view /tmp/V45HaBNwUA/large_chrom.bam ref2:1-541556283
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/V45HaBNwUA/mpileup.bam.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-150
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/V45HaBNwUA/mpileup.bam.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -uv -t DP,DPR,DV,DP4,INFO/DPR,SP -b /tmp/V45HaBNwUA/mpileup.cram.list -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/V45HaBNwUA/mpileup.1.bam | grep -v mpileup
+.. ok
+
+test_mpileup:
+ /«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/V45HaBNwUA/mpileup.ref.fa.gz -r17:1050-1060 /tmp/V45HaBNwUA/mpileup.1.cram | grep -v mpileup
+.. ok
+
+test_usage:
+ samtools
+ samtools has subcommands: faidx, index, calmd, fixmate, reheader, rmdup, targetcut, bamshuf, cat, merge, mpileup, sort, split, bam2fq, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view
+.. ok
+
+test_usage_subcommand:
+ samtools faidx
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools index
+.. ok
+
+test_usage_subcommand:
+ samtools calmd
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools fixmate
+.. ok
+
+test_usage_subcommand:
+ samtools reheader
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools rmdup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools targetcut
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools bamshuf
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools cat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools merge
+.. ok
+
+test_usage_subcommand:
+ samtools mpileup
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools sort
+.. ok
+
+test_usage_subcommand:
+ samtools split
.. ok
-/usr/bin/bgzip -c -b 979200 -s 6 /tmp/OsbUKpLXsb/bgzip.dat.gz
+test_usage_subcommand:
+ samtools bam2fq
.. ok
-/usr/bin/bgzip -c -b 652804 -s 6 /tmp/OsbUKpLXsb/bgzip.dat.gz
+test_usage_subcommand:
+ samtools bedcov
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools depth
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools flagstat
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools idxstats
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools phase
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools stats
.. ok
-Signal caught, cleaning and exiting...
-make[1]: *** [override_dh_auto_test] Terminated
-E: Caught signal ‘Terminated’: terminating immediately
-make[2]: *** [test] Terminated
-make: *** [build-arch] Terminated
-The command failed [15]: /«PKGBUILDDIR»/samtools faidx /tmp/OsbUKpLXsb/faidx.fa
-out:
-err:
- at test/test.pl line 67.
- main::error("The command failed [15]: /«PKGBUILDDIR»/"..., "out:\x{a}", "err:\x{a}") called at test/test.pl line 138
- main::cmd("/«PKGBUILDDIR»/samtools faidx /tmp/OsbUK"...) called at test/test.pl line 390
- main::test_faidx(HASH(0x10030693058)) called at test/test.pl line 36
-debian/rules:18: recipe for target 'override_dh_auto_test' failed
-Makefile:183: recipe for target 'test' failed
-debian/rules:6: recipe for target 'build-arch' failed
-Build killed with signal TERM after 150 minutes of inactivity
+test_usage_subcommand:
+ samtools flags
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools tview
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_usage_subcommand:
+ samtools view
+
+ Usage on stderr rather than stdout
+.. expected failure
+
+test_view:
+ Generating test data file .................. done
+ 1: SAM -> BAM -> SAM .. ok
+
+ 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/V45HaBNwUA/view.001.fogn (SAM input) .. ok
+
+ 50: Count -R /tmp/V45HaBNwUA/view.001.fogn (SAM input) .. ok
+
+ 51: Filter -R /tmp/V45HaBNwUA/view.001.fogn (BAM input) .. ok
+
+ 52: Count -R /tmp/V45HaBNwUA/view.001.fogn (BAM input) .. ok
+
+ 53: Filter -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input) .. ok
+
+ 54: Count -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input) .. ok
+
+ 55: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (SAM input).. ok
+
+ 56: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (SAM input).. ok
+
+ 57: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (BAM input).. ok
+
+ 58: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (BAM input).. ok
+
+ 59: Filter -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 60: Count -R /tmp/V45HaBNwUA/view.001.fogn -r grp2 (CRAM input).. ok
+
+ 61: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (SAM input).. ok
+
+ 62: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (SAM input).. ok
+
+ 63: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (BAM input).. ok
+
+ 64: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (BAM input).. ok
+
+ 65: Filter -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input).. ok
+
+ 66: Count -r grp2 -R /tmp/V45HaBNwUA/view.001.fogn (CRAM input).. ok
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 67: Filter -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/V45HaBNwUA/view.test067.sam -h -l Library 2 /tmp/V45HaBNwUA/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 68: Count -l Library 2 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/V45HaBNwUA/view.001.sam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 69: Filter -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/V45HaBNwUA/view.test069.sam -h -l Library 2 /tmp/V45HaBNwUA/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 70: Count -l Library 2 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/V45HaBNwUA/view.test001.bam
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 71: Filter -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -o /tmp/V45HaBNwUA/view.test071.sam -h -l Library 2 /tmp/V45HaBNwUA/view.test006.cram
+
+
+.. expected failure
+
+Samtools-htslib-API: bam_get_library() not yet implemented
+ 72: Count -l Library 2 (CRAM input) Failed command:
+ /«PKGBUILDDIR»/samtools view -c -l Library 2 /tmp/V45HaBNwUA/view.test006.cram
+
+
+.. expected failure
+
+ 73: Filter -q 50 (SAM input) .. ok
+
+ 74: Count -q 50 (SAM input) .. ok
+
+ 75: Filter -q 50 (BAM input) .. ok
+
+ 76: Count -q 50 (BAM input) .. ok
+
+ 77: Filter -q 50 (CRAM input) .. ok
+
+ 78: Count -q 50 (CRAM input) .. ok
+
+ 79: Filter -q 99 (SAM input) .. ok
+
+ 80: Count -q 99 (SAM input) .. ok
+
+ 81: Filter -q 99 (BAM input) .. ok
+
+ 82: Count -q 99 (BAM input) .. ok
+
+ 83: Filter -q 99 (CRAM input) .. ok
+
+ 84: Count -q 99 (CRAM input) .. ok
+
+ 85: Filter -q 100 (SAM input) .. ok
+
+ 86: Count -q 100 (SAM input) .. ok
+
+ 87: Filter -q 100 (BAM input) .. ok
+
+ 88: Count -q 100 (BAM input) .. ok
+
+ 89: Filter -q 100 (CRAM input) .. ok
+
+ 90: Count -q 100 (CRAM input) .. ok
+
+ 91: Filter -x fa (SAM input) .. ok
+
+ 92: Count -x fa (SAM input) .. ok
+
+ 93: Filter -x fa (BAM input) .. ok
+
+ 94: Count -x fa (BAM input) .. ok
+
+ 95: Filter -x fa (CRAM input) .. ok
+
+ 96: Count -x fa (CRAM input) .. ok
+
+ 97: Filter -x fa -x ha (SAM input) .. ok
+
+ 98: Count -x fa -x ha (SAM input) .. ok
+
+ 99: Filter -x fa -x ha (BAM input) .. ok
+
+ 100: Count -x fa -x ha (BAM input) .. ok
+
+ 101: Filter -x fa -x ha (CRAM input) .. ok
+
+ 102: Count -x fa -x ha (CRAM input) .. ok
+
+ 103: Filter -x fa -r grp2 (SAM input) .. ok
+
+ 104: Count -x fa -r grp2 (SAM input) .. ok
+
+ 105: Filter -x fa -r grp2 (BAM input) .. ok
+
+ 106: Count -x fa -r grp2 (BAM input) .. ok
+
+ 107: Filter -x fa -r grp2 (CRAM input) .. ok
+
+ 108: Count -x fa -r grp2 (CRAM input) .. ok
+
+ 109: Filter -x RG -r grp2 (SAM input) .. ok
+
+ 110: Count -x RG -r grp2 (SAM input) .. ok
+
+ 111: Filter -x RG -r grp2 (BAM input) .. ok
+
+ 112: Count -x RG -r grp2 (BAM input) .. ok
+
+ 113: Filter -x RG -r grp2 (CRAM input) .. ok
+
+ 114: Count -x RG -r grp2 (CRAM input) .. ok
+
+ 115: Filter -m 10 (SAM input) .. ok
+
+ 116: Count -m 10 (SAM input) .. ok
+
+ 117: Filter -m 10 (BAM input) .. ok
+
+ 118: Count -m 10 (BAM input) .. ok
+
+ 119: Filter -m 10 (CRAM input) .. ok
+
+ 120: Count -m 10 (CRAM input) .. ok
+
+ 121: Filter -m 11 (SAM input) .. ok
+
+ 122: Count -m 11 (SAM input) .. ok
+
+ 123: Filter -m 11 (BAM input) .. ok
+
+ 124: Count -m 11 (BAM input) .. ok
+
+ 125: Filter -m 11 (CRAM input) .. ok
+
+ 126: Count -m 11 (CRAM input) .. ok
+
+ 127: Filter -m 15 (SAM input) .. ok
+
+ 128: Count -m 15 (SAM input) .. ok
+
+ 129: Filter -m 15 (BAM input) .. ok
+
+ 130: Count -m 15 (BAM input) .. ok
+
+ 131: Filter -m 15 (CRAM input) .. ok
+
+ 132: Count -m 15 (CRAM input) .. ok
+
+ 133: Filter -m 16 (SAM input) .. ok
+
+ 134: Count -m 16 (SAM input) .. ok
+
+ 135: Filter -m 16 (BAM input) .. ok
+
+ 136: Count -m 16 (BAM input) .. ok
+
+ 137: Filter -m 16 (CRAM input) .. ok
+
+ 138: Count -m 16 (CRAM input) .. ok
+
+ 139: 1bp reads file SAM -> BAM -> SAM .. ok
+
+ 140: 1bp reads file SAM -> CRAM -> SAM .. ok
+
+ 140: Region Z (BAM input) .. ok
+
+ 141: Count Z (BAM input) .. ok
+
+ 142: Region Z (CRAM input) .. ok
+
+ 143: Count Z (CRAM input) .. ok
+
+ 144: Region Z:30 (BAM input) .. ok
+
+ 145: Count Z:30 (BAM input) .. ok
+
+ 146: Region Z:30 (CRAM input) .. ok
+
+ 147: Count Z:30 (CRAM input) .. ok
+
+ 148: Region Z:20-40 (BAM input) .. ok
+
+ 149: Count Z:20-40 (BAM input) .. ok
+
+ 150: Region Z:20-40 (CRAM input) .. ok
+
+ 151: Count Z:20-40 (CRAM input) .. ok
+
+ 152: Region ref1 (BAM input) .. ok
+
+ 153: Count ref1 (BAM input) .. ok
+
+ 154: Region ref1 (CRAM input) .. ok
+
+ 155: Count ref1 (CRAM input) .. ok
+
+ 156: Region ref1:15 (BAM input) .. ok
+
+ 157: Count ref1:15 (BAM input) .. ok
+
+ 158: Region ref1:15 (CRAM input) .. ok
+
+ 159: Count ref1:15 (CRAM input) .. ok
+
+ 160: Region ref1:15-45 (BAM input) .. ok
+
+ 161: Count ref1:15-45 (BAM input) .. ok
+
+ 162: Region ref1:15-45 (CRAM input) .. ok
+
+ 163: Count ref1:15-45 (CRAM input) .. ok
+
+ 164: Region ref1:15-45 ref2 (BAM input) .. ok
+
+ 165: Count ref1:15-45 ref2 (BAM input) .. ok
+
+ 166: Region ref1:15-45 ref2 (CRAM input) .. ok
+
+ 167: Count ref1:15-45 ref2 (CRAM input) .. ok
+
+ 168: Region ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 169: Count ref1:15-45 ref2:16 (BAM input) .. ok
+
+ 170: Region ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 171: Count ref1:15-45 ref2:16 (CRAM input) .. ok
+
+ 172: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 173: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
+
+ 174: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 175: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
+
+ 176: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 177: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
+
+ 178: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 179: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
+
+ 180: Region -f 128 ref1 (BAM input) .. ok
+
+ 181: Count -f 128 ref1 (BAM input) .. ok
+
+ 182: Region -f 128 ref1 (CRAM input) .. ok
+
+ 183: Count -f 128 ref1 (CRAM input) .. ok
+
+ 184: Region -q 50 ref1:15-45 (BAM input) .. ok
+
+ 185: Count -q 50 ref1:15-45 (BAM input) .. ok
+
+ 186: Region -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 187: Count -q 50 ref1:15-45 (CRAM input) .. ok
+
+ 188: Region -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 189: Count -r grp2 ref1:15-45 (BAM input) .. ok
+
+ 190: Region -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 191: Count -r grp2 ref1:15-45 (CRAM input) .. ok
+
+ 192: 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
+
+ 194: 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
+
+ 196: 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
+
+ 198: 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
+
+ 200: 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
+
+ 202: 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
+
+ 204: 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
+
+ 206: 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
+
+ 208: 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
+
+ 210: 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
+
+ 212: 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
+
+ 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:30 (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:10-30 (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:10-30 (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:25-35 (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:25-35 (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.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
+
+ 227: 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
+
+ 229: 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
+
+ 231: 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
+
+ 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 -r grp1 (CRAM 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 -f 128 (BAM 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 -f 128 (CRAM 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 -q 5 (BAM 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 -q 5 (CRAM 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 -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
+
+ 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 -r grp1 ref1:11-16 (CRAM input).. ok
+
+ 248: Make BAM with no M5/UR tags .. ok
+
+ 249: Add @SQ with -t (SAM -> SAM) .. ok
+
+ 250: Add @SQ with -T (SAM -> SAM) .. ok
+
+ 251: Add @SQ with -t (BAM -> SAM) .. ok
+
+ 252: Add @SQ with -T (BAM -> SAM) .. ok
+
+ 253: Add @SQ with -t (SAM -> BAM) .. ok
+
+ 254: Add @SQ with -T (SAM -> BAM) .. ok
+
+ 255: Add @SQ with -t (BAM -> BAM) .. ok
+
+ 256: Add @SQ with -T (BAM -> BAM) .. ok
+
+ 257: Add @SQ with -t (SAM -> CRAM) .. ok
+
+ 258: Add @SQ with -T (SAM -> CRAM) .. ok
+
+ 259: Add @SQ with -t (BAM -> CRAM) .. ok
+
+ 260: Add @SQ with -T (BAM -> CRAM) .. ok
+
+ 261: Make CRAM with no UR field .. ok
+
+ 262: Decoding CRAM with no UR field via -T .. ok
+
+ 263: CIGAR B-operator removal .. ok
+
+ 264: Big SAM -> BAM .. ok
+
+ 265: Big SAM -> BAM (2 threads) .. ok
+
+ 266: Big SAM -> BAM (4 threads) .. ok
+
+ 267: Big SAM -> CRAM .. ok
+
+ 268: Big SAM -> CRAM (2 threads) .. ok
+
+ 269: Big SAM -> CRAM (4 threads) .. ok
+
+ 270: Subsample 0.2 (SAM input) ............ ok
+
+ 271: Subsample 0.5 (SAM input) ............ ok
+
+ 272: Subsample 0.8 (SAM input) ............ ok
+
+ 273: Subsample 0.2 (BAM input) ............ ok
+
+ 274: Subsample 0.5 (BAM input) ............ ok
+
+ 275: Subsample 0.8 (BAM input) ............ ok
+
+ 276: Subsample 0.2 (CRAM input) ............ ok
+
+ 277: Subsample 0.5 (CRAM input) ............ ok
+
+ 278: Subsample 0.8 (CRAM input) ............ ok
+
+test_cat:
+ Generating test data file .................. done
+ Generate BAM file #1 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #2 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #3 .. ok
+
+ Generating test data file .................. done
+ Generate BAM file #4 .. ok
+
+ 1: cat BAM files .. ok
+
+ 2: cat recompressed BAM files .. ok
+
+ 3: cat BAM files to stdout .. ok
+
+ 4: cat recompressed BAM files to stdout .. ok
+
+ 5: cat BAM files with new header .. ok
+
+ 6: cat recompressed BAM files with new header .. ok
+
+test_bam2fq:
+ Generate BAM file .. ok
+
+Unsorted mode enabled
+ Generate CRAM file .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 1: bam2fq (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 2: bam2fq -n (SAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 3: bam2fq (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 4: bam2fq -n (BAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 5: bam2fq (CRAM input) .. ok
+
+[M::main_bam2fq] processed 36 reads
+ 6: bam2fq -n (CRAM input) .. ok
+
+test_depad:
+ Generate BAM file .. ok
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (SAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /«PKGBUILDDIR»/test/dat/depad.001p.sam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa /tmp/V45HaBNwUA/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -s (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -s /tmp/V45HaBNwUA/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -u (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -u /tmp/V45HaBNwUA/depad.001p.bam
+
+
+.. expected failure
+
+Samtools-htslib: fix_header() header parsing not yet implemented
+ depad -1 (BAM input) Failed command:
+ /«PKGBUILDDIR»/samtools depad -T /«PKGBUILDDIR»/test/dat/depad.001.fa -1 /tmp/V45HaBNwUA/depad.001p.bam
+
+
+.. expected failure
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/1_map_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/2_equal_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/3_map_cigar_equal_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/4_X_cigar_full_seq.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. ok
+
+test_stats:
+ /«PKGBUILDDIR»/samtools stats -r /«PKGBUILDDIR»/test/stat/test.fa -i 0 /«PKGBUILDDIR»/test/stat/5_insert_cigar.sam | tail -n+3
+.. 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/FMbWO6d3XC - /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+test_fixmate:
+ /«PKGBUILDDIR»/samtools fixmate -O sam /«PKGBUILDDIR»/test/fixmate/1_coord_sort.sam -
+
+.. 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
+
+test_idxstat:
+ /«PKGBUILDDIR»/samtools idxstats /«PKGBUILDDIR»/test/dat/test_input_1_a.bam
+.. ok
+
+
+Number of tests:
+ total .. 368
+ passed .. 336
+ failed .. 0
+ expected failure .. 32
+ unexpected pass .. 0
+
+test/merge/test_bam_translate test/merge/test_bam_translate.tmp
+test/merge/test_pretty_header
+test/merge/test_rtrans_build
+test/merge/test_trans_tbl_init
+cd test/mpileup && ./regression.sh
+Samtools mpileup tests:
+
+EXPECTED FAIL: Task failed, but expected to fail;
+when running $samtools mpileup -x -d 8500 -B -f mpileup.ref.fa deep.sam|awk '{print $4}'
+
+Expected passes: 123
+Unexpected passes: 0
+Expected failures: 1
+Unexpected failures: 0
+=> PASS
+test/split/test_count_rg
+test/split/test_expand_format_string
+test/split/test_filter_header_rg
+test/split/test_parse_args
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a
+ install -d debian/samtools
+ make -j4 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/powerpc64le-linux-gnu/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/powerpc64le-linux-gnu/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_ppc64el.deb'.
+ dpkg-genchanges -B -mppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org> >../samtools_1.2-3_ppc64el.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
-Build finished at 20140925-0455
+Build finished at 20150922-1614
Finished
────────
-E: Build failure (dpkg-buildpackage died)
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_ppc64el.changes:
+───────────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: ppc64el
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: ppc64el Build Daemon (ppc64el-osuosl-01) <buildd_ppc64el-ppc64el-osuosl-01 at buildd.debian.org>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ 7baa0c425137bb89ec61606ee03386e7ad27fd62 376902 samtools_1.2-3_ppc64el.deb
+Checksums-Sha256:
+ f6d8ae5f0f5184a7e6f313141e5b17be430381e876aa5a1f04c2b4819fb86ff3 376902 samtools_1.2-3_ppc64el.deb
+Files:
+ 7ea932e83a5844dc64981b8a7ab520ef 376902 science optional samtools_1.2-3_ppc64el.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_ppc64el.deb
+──────────────────────────
+
+ new debian package, version 2.0.
+ size 376902 bytes: control archive=1489 bytes.
+ 805 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: ppc64el
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1485
+ Depends: libc6 (>= 2.17), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ Recommends: python
+ Section: science
+ Priority: optional
+ Homepage: http://www.htslib.org/
+ Description: processing sequence alignments in SAM and BAM formats
+ Samtools is a set of utilities that manipulate nucleotide sequence alignments
+ in the binary BAM format. It imports from and exports to the ascii SAM
+ (Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/bin/
+-rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 15:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 15:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 15:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 15:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 67680 2015-09-22 16:14 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 67672 2015-09-22 16:14 ./usr/bin/md5fa
+-rwxr-xr-x root/root 67672 2015-09-22 16:14 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 15:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 15:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 15:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 15:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 920504 2015-09-22 16:14 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 15:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 15:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 15:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 15:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 67768 2015-09-22 16:14 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 14:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 14:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 14:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 14:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 16:14 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 16:14 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
@@ -527,20 +1710,23 @@ Not cleaning session: cloned chroot in use
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: ppc64el
-Build-Space: 44608
-Build-Time: 9005
+Build-Space: 35892
+Build-Time: 199
Distribution: sid
-Fail-Stage: build
Host Architecture: ppc64el
-Install-Time: 9
-Job: samtools_1.1-1
+Install-Time: 8
+Job: samtools_1.2-3
Machine Architecture: ppc64el
Package: samtools
-Package-Time: 9026
-Source-Version: 1.1-1
-Space: 44608
-Status: attempted
-Version: 1.1-1
+Package-Time: 225
+Source-Version: 1.2-3
+Space: 35892
+Status: successful
+Version: 1.2-3
────────────────────────────────────────────────────────────────────────────────
-Finished at 20140925-0455
-Build needed 02:30:26, 44608k disc space
+Finished at 20150922-1614
+Build needed 00:03:45, 35892k disc space
+Signature with key 'AE6C7FBC' requested:
+ signfile /home/buildd/build/samtools_1.2-3_ppc64el.changes AE6C7FBC
+
+Successfully signed changes file
diff --git a/s390.log b/s390.log
deleted file mode 100644
index a3ec27a..0000000
--- a/s390.log
+++ /dev/null
@@ -1,1798 +0,0 @@
-From buildd at zandonai.debian.org Sat Mar 30 09:17:45 2013
-Return-path: <buildd at zandonai.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at zandonai.debian.org>)
- id 1ULruy-0002aJ-S8
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:17:45 +0000
-Received: from zandonai.debian.org ([80.245.147.46])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zandonai.debian.org,
- EMAIL=hostmaster at zandonai.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at zandonai.debian.org>)
- id 1ULruv-0007Rf-J7; Sat, 30 Mar 2013 09:17:42 +0000
-Received: from buildd by zandonai.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zandonai.debian.org>)
- id 1ULrut-0004a6-2O; Sat, 30 Mar 2013 09:17:39 +0000
-Message-Id: <E1ULrut-0004a6-2O at zandonai.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:17:39 +0000
-From: buildd on zandonai <buildd at zandonai.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on s390 (dist=sid)
-Key-Id: B6E651D0
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zandonai.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (s390) 30 Mar 2013 09:16 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: s390
-Get:1 http://ftp.de.debian.org unstable Release.gpg [836 B]
-Get:2 http://ftp.de.debian.org unstable Release [235 kB]
-Get:3 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:4 http://ftp.de.debian.org unstable/main Sources [6484 kB]
-Get:5 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:6 http://incoming.debian.org unstable Release [235 kB]
-Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:9 http://ftp.de.debian.org unstable/contrib Sources [51.0 kB]
-Get:10 http://ftp.de.debian.org unstable/non-free Sources [101 kB]
-Get:11 http://ftp.de.debian.org unstable/main s390 Packages [6043 kB]
-Get:12 http://ftp.de.debian.org unstable/contrib s390 Packages [35.3 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main s390 Packages [6043 kB]
-Get:16 http://incoming.debian.org unstable/contrib s390 Packages [35.3 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main s390 Packages [13.1 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib s390 Packages [14 B]
-Fetched 26.0 MB in 24s (1072 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (370 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 6 not upgraded.
-Need to get 10.2 MB of archives.
-After this operation, 30.0 MB of additional disk space will be used.
-Get:1 http://ftp.de.debian.org/debian/ unstable/main libpipeline1 s390 1.2.2-2 [40.6 kB]
-Get:2 http://ftp.de.debian.org/debian/ unstable/main groff-base s390 1.22.2-1 [713 kB]
-Get:3 http://ftp.de.debian.org/debian/ unstable/main bsdmainutils s390 9.0.4 [214 kB]
-Get:4 http://ftp.de.debian.org/debian/ unstable/main man-db s390 2.6.3-3 [884 kB]
-Get:5 http://ftp.de.debian.org/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp.de.debian.org/debian/ unstable/main libasprintf0c2 s390 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp.de.debian.org/debian/ unstable/main libmagic1 s390 1:5.11-2.1 [205 kB]
-Get:8 http://ftp.de.debian.org/debian/ unstable/main libpcre3 s390 1:8.31-2 [253 kB]
-Get:9 http://ftp.de.debian.org/debian/ unstable/main libxml2 s390 2.8.0+dfsg1-7+nmu1 [892 kB]
-Get:10 http://ftp.de.debian.org/debian/ unstable/main libffi5 s390 3.0.10-3 [25.3 kB]
-Get:11 http://ftp.de.debian.org/debian/ unstable/main libglib2.0-0 s390 2.33.12+really2.32.4-5 [1788 kB]
-Get:12 http://ftp.de.debian.org/debian/ unstable/main libcroco3 s390 0.6.6-2 [128 kB]
-Get:13 http://ftp.de.debian.org/debian/ unstable/main libunistring0 s390 0.9.3-5 [433 kB]
-Get:14 http://ftp.de.debian.org/debian/ unstable/main libgettextpo0 s390 0.18.1.1-10 [147 kB]
-Get:15 http://ftp.de.debian.org/debian/ unstable/main file s390 1:5.11-2.1 [52.1 kB]
-Get:16 http://ftp.de.debian.org/debian/ unstable/main gettext-base s390 0.18.1.1-10 [152 kB]
-Get:17 http://ftp.de.debian.org/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp.de.debian.org/debian/ unstable/main html2text s390 1.3.2a-15 [101 kB]
-Get:19 http://ftp.de.debian.org/debian/ unstable/main libasprintf-dev s390 0.18.1.1-10 [27.1 kB]
-Get:20 http://ftp.de.debian.org/debian/ unstable/main libgettextpo-dev s390 0.18.1.1-10 [182 kB]
-Get:21 http://ftp.de.debian.org/debian/ unstable/main gettext s390 0.18.1.1-10 [1800 kB]
-Get:22 http://ftp.de.debian.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp.de.debian.org/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp.de.debian.org/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp.de.debian.org/debian/ unstable/main diffstat s390 1.55-3 [29.8 kB]
-Get:26 http://ftp.de.debian.org/debian/ unstable/main libtinfo-dev s390 5.9-10 [113 kB]
-Get:27 http://ftp.de.debian.org/debian/ unstable/main libncurses5-dev s390 5.9-10 [213 kB]
-Get:28 http://ftp.de.debian.org/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp.de.debian.org/debian/ unstable/main zlib1g-dev s390 1:1.2.7.dfsg-13 [215 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.2 MB in 3s (3278 kB/s)
-Selecting previously unselected package libpipeline1:s390.
-(Reading database ... 10740 files and directories currently installed.)
-Unpacking libpipeline1:s390 (from .../libpipeline1_1.2.2-2_s390.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_s390.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_s390.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_s390.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:s390.
-Unpacking libasprintf0c2:s390 (from .../libasprintf0c2_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package libmagic1:s390.
-Unpacking libmagic1:s390 (from .../libmagic1_1%3a5.11-2.1_s390.deb) ...
-Selecting previously unselected package libpcre3:s390.
-Unpacking libpcre3:s390 (from .../libpcre3_1%3a8.31-2_s390.deb) ...
-Selecting previously unselected package libxml2:s390.
-Unpacking libxml2:s390 (from .../libxml2_2.8.0+dfsg1-7+nmu1_s390.deb) ...
-Selecting previously unselected package libffi5:s390.
-Unpacking libffi5:s390 (from .../libffi5_3.0.10-3_s390.deb) ...
-Selecting previously unselected package libglib2.0-0:s390.
-Unpacking libglib2.0-0:s390 (from .../libglib2.0-0_2.33.12+really2.32.4-5_s390.deb) ...
-Selecting previously unselected package libcroco3:s390.
-Unpacking libcroco3:s390 (from .../libcroco3_0.6.6-2_s390.deb) ...
-Selecting previously unselected package libunistring0:s390.
-Unpacking libunistring0:s390 (from .../libunistring0_0.9.3-5_s390.deb) ...
-Selecting previously unselected package libgettextpo0:s390.
-Unpacking libgettextpo0:s390 (from .../libgettextpo0_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_s390.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_s390.deb) ...
-Selecting previously unselected package libasprintf-dev:s390.
-Unpacking libasprintf-dev:s390 (from .../libasprintf-dev_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package libgettextpo-dev:s390.
-Unpacking libgettextpo-dev:s390 (from .../libgettextpo-dev_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_s390.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_s390.deb) ...
-Selecting previously unselected package libtinfo-dev:s390.
-Unpacking libtinfo-dev:s390 (from .../libtinfo-dev_5.9-10_s390.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:s390.
-Unpacking zlib1g-dev:s390 (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390.deb) ...
-Setting up libpipeline1:s390 (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:s390 (0.18.1.1-10) ...
-Setting up libmagic1:s390 (1:5.11-2.1) ...
-Setting up libpcre3:s390 (1:8.31-2) ...
-Setting up libxml2:s390 (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:s390 (3.0.10-3) ...
-Setting up libglib2.0-0:s390 (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390 (0.6.6-2) ...
-Setting up libunistring0:s390 (0.9.3-5) ...
-Setting up libgettextpo0:s390 (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:s390 (0.18.1.1-10) ...
-Setting up libgettextpo-dev:s390 (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:s390 (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:s390 (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 6 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-s390x s390 (s390x)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 fakeroot_1.18.4-2 [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture s390
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390-TTe7pN/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_s390.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_s390.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org> >../samtools_0.1.19-1_s390.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0917
-
-samtools_0.1.19-1_s390.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: s390
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: s390/s390x Build Daemon (zandonai) <buildd_s390-zandonai at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- b3bd6cd9c24ec4850474f6634a58edc446ef7442 558568 samtools_0.1.19-1_s390.deb
- ad9c7a43cb6be3006c9786bcf3e0a5b172a484c0 124686 libbam-dev_0.1.19-1_s390.deb
-Checksums-Sha256:
- 193cd1de13932b41c6b5cb54c63457c7fdcb67683ed01cc25a3d9b38f7ae8096 558568 samtools_0.1.19-1_s390.deb
- f575369d52f329061d6f354b1a2bf20603572c68ecb65105ef1c2f3ffb6f738d 124686 libbam-dev_0.1.19-1_s390.deb
-Files:
- e6a78223f763b1c03642bf878a27185e 558568 science optional samtools_0.1.19-1_s390.deb
- 153c42643e10f72b7617f80ce957c285 124686 libdevel optional libbam-dev_0.1.19-1_s390.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_s390.deb
-──────────────────────────
-
- new debian package, version 2.0.
- size 558568 bytes: control archive= 1932 bytes.
- 32 bytes, 1 lines conffiles
- 791 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1398
- Depends: libc6 (>= 2.7), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
--rwxr-xr-x root/root 165852 2013-03-30 09:17 ./usr/bin/bcftools
--rwxr-xr-x root/root 464120 2013-03-30 09:17 ./usr/bin/samtools
--rwxr-xr-x root/root 30216 2013-03-30 09:17 ./usr/bin/razip
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
--rwxr-xr-x root/root 13680 2013-03-30 09:17 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 17796 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 9592 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 9592 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
--rwxr-xr-x root/root 9556 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 17868 2013-03-30 09:17 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 199656 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
--rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
--rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_s390.deb
-────────────────────────────
-
- new debian package, version 2.0.
- size 124686 bytes: control archive= 922 bytes.
- 711 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: s390
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 399
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
--rw-r--r-- root/root 286026 2013-03-30 09:17 ./usr/lib/libbam.a
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-s390-sbuild-296b5c29-f621-4e79-8986-bd8896aed292/build/buildd-samtools_0.1.19-1-s390-TTe7pN
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: s390
-Build-Space: 13264
-Build-Time: 34
-Distribution: sid
-Install-Time: 11
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 80
-Source-Version: 0.1.19-1
-Space: 13264
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0917
-Build needed 00:01:20, 13264k disc space
-Signature with key 'B6E651D0' requested:
-From buildd at zemlinsky.debian.org Sat Mar 30 09:17:41 2013
-Return-path: <buildd at zemlinsky.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
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- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
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-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:17:34 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on s390x (dist=sid)
-Key-Id: 52DC96B8
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (s390x) 30 Mar 2013 09:15 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: s390x
-Hit http://ftp-stud.hs-esslingen.de unstable Release.gpg
-Hit http://ftp-stud.hs-esslingen.de unstable Release
-Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
-Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
-Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:4 http://incoming.debian.org unstable Release [235 kB]
-Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:7 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:8 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:9 http://incoming.debian.org unstable/main s390x Packages [6017 kB]
-Get:10 http://incoming.debian.org unstable/contrib s390x Packages [35.3 kB]
-Get:11 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:12 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:13 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:14 http://incoming.debian.org buildd-unstable/main s390x Packages [13.1 kB]
-Get:15 http://incoming.debian.org buildd-unstable/contrib s390x Packages [14 B]
-Fetched 13.2 MB in 9s (1356 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (342 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 11 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 31.6 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-2 [41.1 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.22.2-1+b1 [738 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.4 [215 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 1:5.11-2.1 [201 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-2 [259 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7+nmu1 [902 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-5 [1798 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 1:5.11-2.1 [52.0 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-10 [1864 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
-Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 1s (9424 kB/s)
-Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10875 files and directories currently installed.)
-Unpacking libpipeline1:s390x (from .../libpipeline1_1.2.2-2_s390x.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1+b1_s390x.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_s390x.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_s390x.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:s390x.
-Unpacking libasprintf0c2:s390x (from .../libasprintf0c2_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package libmagic1:s390x.
-Unpacking libmagic1:s390x (from .../libmagic1_1%3a5.11-2.1_s390x.deb) ...
-Selecting previously unselected package libpcre3:s390x.
-Unpacking libpcre3:s390x (from .../libpcre3_1%3a8.31-2_s390x.deb) ...
-Selecting previously unselected package libxml2:s390x.
-Unpacking libxml2:s390x (from .../libxml2_2.8.0+dfsg1-7+nmu1_s390x.deb) ...
-Selecting previously unselected package libffi5:s390x.
-Unpacking libffi5:s390x (from .../libffi5_3.0.10-3+b1_s390x.deb) ...
-Selecting previously unselected package libglib2.0-0:s390x.
-Unpacking libglib2.0-0:s390x (from .../libglib2.0-0_2.33.12+really2.32.4-5_s390x.deb) ...
-Selecting previously unselected package libcroco3:s390x.
-Unpacking libcroco3:s390x (from .../libcroco3_0.6.6-2_s390x.deb) ...
-Selecting previously unselected package libunistring0:s390x.
-Unpacking libunistring0:s390x (from .../libunistring0_0.9.3-5+b1_s390x.deb) ...
-Selecting previously unselected package libgettextpo0:s390x.
-Unpacking libgettextpo0:s390x (from .../libgettextpo0_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_s390x.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15+b1_s390x.deb) ...
-Selecting previously unselected package libasprintf-dev:s390x.
-Unpacking libasprintf-dev:s390x (from .../libasprintf-dev_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package libgettextpo-dev:s390x.
-Unpacking libgettextpo-dev:s390x (from .../libgettextpo-dev_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_s390x.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_s390x.deb) ...
-Selecting previously unselected package libtinfo-dev:s390x.
-Unpacking libtinfo-dev:s390x (from .../libtinfo-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_s390x.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:s390x.
-Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.2-2) ...
-Setting up groff-base (1.22.2-1+b1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
-Setting up libmagic1:s390x (1:5.11-2.1) ...
-Setting up libpcre3:s390x (1:8.31-2) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390x (0.6.6-2) ...
-Setting up libunistring0:s390x (0.9.3-5+b1) ...
-Setting up libgettextpo0:s390x (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
-Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:s390x (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture s390x
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_s390x.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.19-1_s390x.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0917
-
-samtools_0.1.19-1_s390x.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: s390x
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 44b0ad7015c66de7ea61172247a7884218c5b8aa 560790 samtools_0.1.19-1_s390x.deb
- 884eb297e57fc14d47b73d4655e291f6fc9ff0c3 122144 libbam-dev_0.1.19-1_s390x.deb
-Checksums-Sha256:
- 8764098ec4269510b9054964c3ca0ebff7c1324ece301d60f210457d23150f54 560790 samtools_0.1.19-1_s390x.deb
- 3afb93b0941f94245f8f25c53d68d10cd5d425e46769655e1a396442e4afc034 122144 libbam-dev_0.1.19-1_s390x.deb
-Files:
- 13d6e54829d787f92d2d384d1febce1e 560790 science optional samtools_0.1.19-1_s390x.deb
- af7829858681083a1704e14e55263cd6 122144 libdevel optional libbam-dev_0.1.19-1_s390x.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_s390x.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 560790 bytes: control archive= 1937 bytes.
- 32 bytes, 1 lines conffiles
- 793 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: s390x
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1452
- Depends: libc6 (>= 2.13), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
--rwxr-xr-x root/root 494752 2013-03-30 09:17 ./usr/bin/samtools
--rwxr-xr-x root/root 175256 2013-03-30 09:17 ./usr/bin/bcftools
--rwxr-xr-x root/root 31136 2013-03-30 09:17 ./usr/bin/razip
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
--rwxr-xr-x root/root 22768 2013-03-30 09:17 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10272 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 22656 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 14424 2013-03-30 09:17 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 201392 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_s390x.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 122144 bytes: control archive= 924 bytes.
- 712 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: s390x
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 461
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
--rw-r--r-- root/root 349450 2013-03-30 09:17 ./usr/lib/libbam.a
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-683aa926-ac15-426d-91c5-f4f101ce8fb3/build/buildd-samtools_0.1.19-1-s390x-JVvJbf
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: s390x
-Build-Space: 15508
-Build-Time: 65
-Distribution: sid
-Install-Time: 15
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 97
-Source-Version: 0.1.19-1
-Space: 15508
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0917
-Build needed 00:01:37, 15508k disc space
-Signature with key '52DC96B8' requested:
diff --git a/s390x.log b/s390x.log
deleted file mode 100644
index 90f21ac..0000000
--- a/s390x.log
+++ /dev/null
@@ -1,905 +0,0 @@
-From buildd at zemlinsky.debian.org Sat Mar 30 09:17:41 2013
-Return-path: <buildd at zemlinsky.debian.org>
-Received: from muffat.debian.org ([206.12.19.146])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=muffat.debian.org, EMAIL=hostmaster at muffat.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:DHE_RSA_AES_128_CBC_SHA1:16)
- (Exim 4.72) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1ULruv-0002ZT-20
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:17:41 +0000
-Received: from zemlinsky.debian.org ([129.143.160.6])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=zemlinsky.debian.org,
- EMAIL=hostmaster at zemlinsky.debian.org (verified)
- by muffat.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:256)
- (Exim 4.80) (envelope-from <buildd at zemlinsky.debian.org>)
- id 1ULruq-0007Ra-Sh; Sat, 30 Mar 2013 09:17:37 +0000
-Received: from buildd by zemlinsky.debian.org with local (Exim 4.72)
- (envelope-from <buildd at zemlinsky.debian.org>)
- id 1ULruo-0004v0-E5; Sat, 30 Mar 2013 09:17:34 +0000
-Message-Id: <E1ULruo-0004v0-E5 at zemlinsky.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:17:34 +0000
-From: buildd on zemlinsky <buildd at zemlinsky.debian.org>
-To: phil+buildd at philkern.de,logs at buildd.debian.org
-Subject: Log for successful build of samtools_0.1.19-1 on s390x (dist=sid)
-Key-Id: 52DC96B8
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on zemlinsky.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (s390x) 30 Mar 2013 09:15 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: s390x
-Hit http://ftp-stud.hs-esslingen.de unstable Release.gpg
-Hit http://ftp-stud.hs-esslingen.de unstable Release
-Hit http://ftp-stud.hs-esslingen.de unstable/main Sources
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib Sources
-Get:1 http://ftp-stud.hs-esslingen.de unstable/non-free Sources [101 kB]
-Hit http://ftp-stud.hs-esslingen.de unstable/main s390x Packages
-Hit http://ftp-stud.hs-esslingen.de unstable/contrib s390x Packages
-Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:4 http://incoming.debian.org unstable Release [235 kB]
-Get:5 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:6 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:7 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:8 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:9 http://incoming.debian.org unstable/main s390x Packages [6017 kB]
-Get:10 http://incoming.debian.org unstable/contrib s390x Packages [35.3 kB]
-Get:11 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:12 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:13 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:14 http://incoming.debian.org buildd-unstable/main s390x Packages [13.1 kB]
-Get:15 http://incoming.debian.org buildd-unstable/contrib s390x Packages [14 B]
-Fetched 13.2 MB in 9s (1356 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (342 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.20-3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.9)
-e2fsprogs: already installed (1.42.5-1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.9 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 11 not upgraded.
-Need to get 10.4 MB of archives.
-After this operation, 31.6 MB of additional disk space will be used.
-Get:1 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpipeline1 s390x 1.2.2-2 [41.1 kB]
-Get:2 http://ftp-stud.hs-esslingen.de/debian/ unstable/main groff-base s390x 1.22.2-1+b1 [738 kB]
-Get:3 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bsdmainutils s390x 9.0.4 [215 kB]
-Get:4 http://ftp-stud.hs-esslingen.de/debian/ unstable/main man-db s390x 2.6.3-3 [888 kB]
-Get:5 http://ftp-stud.hs-esslingen.de/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf0c2 s390x 0.18.1.1-10 [27.2 kB]
-Get:7 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libmagic1 s390x 1:5.11-2.1 [201 kB]
-Get:8 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libpcre3 s390x 1:8.31-2 [259 kB]
-Get:9 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libxml2 s390x 2.8.0+dfsg1-7+nmu1 [902 kB]
-Get:10 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libffi5 s390x 3.0.10-3+b1 [26.2 kB]
-Get:11 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libglib2.0-0 s390x 2.33.12+really2.32.4-5 [1798 kB]
-Get:12 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libcroco3 s390x 0.6.6-2 [129 kB]
-Get:13 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libunistring0 s390x 0.9.3-5+b1 [442 kB]
-Get:14 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo0 s390x 0.18.1.1-10 [158 kB]
-Get:15 http://ftp-stud.hs-esslingen.de/debian/ unstable/main file s390x 1:5.11-2.1 [52.0 kB]
-Get:16 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext-base s390x 0.18.1.1-10 [156 kB]
-Get:17 http://ftp-stud.hs-esslingen.de/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://ftp-stud.hs-esslingen.de/debian/ unstable/main html2text s390x 1.3.2a-15+b1 [111 kB]
-Get:19 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libasprintf-dev s390x 0.18.1.1-10 [26.8 kB]
-Get:20 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libgettextpo-dev s390x 0.18.1.1-10 [195 kB]
-Get:21 http://ftp-stud.hs-esslingen.de/debian/ unstable/main gettext s390x 0.18.1.1-10 [1864 kB]
-Get:22 http://ftp-stud.hs-esslingen.de/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://ftp-stud.hs-esslingen.de/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://ftp-stud.hs-esslingen.de/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://ftp-stud.hs-esslingen.de/debian/ unstable/main diffstat s390x 1.55-3 [30.5 kB]
-Get:26 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libtinfo-dev s390x 5.9-10 [121 kB]
-Get:27 http://ftp-stud.hs-esslingen.de/debian/ unstable/main libncurses5-dev s390x 5.9-10 [229 kB]
-Get:28 http://ftp-stud.hs-esslingen.de/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://ftp-stud.hs-esslingen.de/debian/ unstable/main zlib1g-dev s390x 1:1.2.7.dfsg-13 [219 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 10.4 MB in 1s (9424 kB/s)
-Selecting previously unselected package libpipeline1:s390x.
-(Reading database ... 10875 files and directories currently installed.)
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-Unpacking zlib1g-dev:s390x (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_s390x.deb) ...
-Setting up libpipeline1:s390x (1.2.2-2) ...
-Setting up groff-base (1.22.2-1+b1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:s390x (0.18.1.1-10) ...
-Setting up libmagic1:s390x (1:5.11-2.1) ...
-Setting up libpcre3:s390x (1:8.31-2) ...
-Setting up libxml2:s390x (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:s390x (3.0.10-3+b1) ...
-Setting up libglib2.0-0:s390x (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:s390x (0.6.6-2) ...
-Setting up libunistring0:s390x (0.9.3-5+b1) ...
-Setting up libgettextpo0:s390x (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15+b1) ...
-Setting up libasprintf-dev:s390x (0.18.1.1-10) ...
-Setting up libgettextpo-dev:s390x (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
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-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:s390x (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:s390x (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following package was automatically installed and is no longer required:
- libapt-pkg4.12
-Use 'apt-get autoremove' to remove it.
-0 upgraded, 0 newly installed, 0 to remove and 11 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-s390x s390x (s390x)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.9 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.20-3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.9 dpkg-dev_1.16.9 e2fslibs_1.42.5-1 e2fsprogs_1.42.5-1 [...]
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-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
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-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture s390x
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-../samtools index ex1.bam
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"a";print}}' | ../samtools view -bS - > ex1a.bam
-[samopen] SAM header is present: 2 sequences.
-../samtools view -h ex1.bam | awk 'BEGIN{FS=OFS="\t"}{if(/^@/)print;else{$1=$1"b";print}}' | ../samtools view -bS - > ex1b.bam
-[samopen] SAM header is present: 2 sequences.
-(echo "@RG ID:ex1 LB:ex1 SM:ex1"; echo "@RG ID:ex1a LB:ex1 SM:ex1"; echo "@RG ID:ex1b LB:ex1b SM:ex1b") > ex1f.rg
-../samtools merge -rh ex1f.rg ex1f.bam ex1.bam ex1a.bam ex1b.bam
-../samtools rmdup ex1f.bam ex1f-rmduppe.bam
-[bam_rmdup_core] processing reference seq1...
-[bam_rmdup_core] processing reference seq2...
-[bam_rmdup_core] 1572 / 3144 = 0.5000 in library 'ex1'
-[bam_rmdup_core] 0 / 1572 = 0.0000 in library 'ex1b'
-../samtools rmdup -S ex1f.bam ex1f-rmdupse.bam
-[bam_rmdupse_core] 4145 / 6542 = 0.6336 in library 'ex1'
-[bam_rmdupse_core] 874 / 3271 = 0.2672 in library 'ex1b'
-../samtools mpileup -gf ex1.fa ex1.bam > ex1.bcf
-[mpileup] 1 samples in 1 input files
-<mpileup> Set max per-file depth to 8000
-gcc -g -Wall -O2 -I.. calDepth.c -o calDepth -L.. -lbam -lm -lz -lpthread
-
-# You can now launch the viewer with: 'samtools tview ex1.bam ex1.fa'
-
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/examples'
-touch debian/stamp-makefile-check
- fakeroot debian/rules binary-arch
-test -x debian/rules
-dh_testroot
-dh_prep
-dh_installdirs -A
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk common-install target
-Adding cdbs dependencies to debian/samtools.substvars
-dh_installdirs -psamtools
-Adding cdbs dependencies to debian/libbam-dev.substvars
-dh_installdirs -plibbam-dev
-dh_installdocs -psamtools ./NEWS ./AUTHORS
-dh_installexamples -psamtools
-dh_installman -psamtools
-dh_installinfo -psamtools
-dh_installmenu -psamtools
-dh_installcron -psamtools
-dh_installinit -psamtools
-dh_installdebconf -psamtools
-dh_installemacsen -psamtools
-dh_installcatalogs -psamtools
-dh_installpam -psamtools
-dh_installlogrotate -psamtools
-dh_installlogcheck -psamtools
-dh_installchangelogs -psamtools NEWS
-dh_installudev -psamtools
-dh_lintian -psamtools
-dh_bugfiles -psamtools
-dh_install -psamtools
-dh_link -psamtools
-dh_installmime -psamtools
-dh_installgsettings -psamtools
-install -m 644 bcftools/README /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/doc/samtools/README.bcftools
-ln -s samtools.1.gz /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/man/man1/bcftools.1.gz
-dh_bash-completion
-dh_bash-completion: file-list parsing failed, installing as proper snippet
-dh_installdocs -plibbam-dev ./NEWS ./AUTHORS
-dh_installexamples -plibbam-dev
-dh_installman -plibbam-dev
-dh_installinfo -plibbam-dev
-dh_installmenu -plibbam-dev
-dh_installcron -plibbam-dev
-dh_installinit -plibbam-dev
-dh_installdebconf -plibbam-dev
-dh_installemacsen -plibbam-dev
-dh_installcatalogs -plibbam-dev
-dh_installpam -plibbam-dev
-dh_installlogrotate -plibbam-dev
-dh_installlogcheck -plibbam-dev
-dh_installchangelogs -plibbam-dev NEWS
-dh_installudev -plibbam-dev
-dh_lintian -plibbam-dev
-dh_bugfiles -plibbam-dev
-dh_install -plibbam-dev
-dh_link -plibbam-dev
-dh_installmime -plibbam-dev
-dh_installgsettings -plibbam-dev
-dh_strip -psamtools
-dh_compress -psamtools -X .bam
-dh_fixperms -psamtools
-dh_makeshlibs -psamtools
-sed -i 's|^#!/software/bin/python|#!/usr/bin/python|' /build/buildd-samtools_0.1.19-1-s390x-JVvJbf/samtools-0.1.19/debian/samtools/usr/share/samtools/varfilter.py
-dh_strip -plibbam-dev
-dh_compress -plibbam-dev -X .bam
-dh_fixperms -plibbam-dev
-dh_makeshlibs -plibbam-dev
-dh_installdeb -psamtools
-dh_perl -psamtools
-dh_shlibdeps -psamtools
-dh_installdeb -plibbam-dev
-dh_perl -plibbam-dev
-dh_shlibdeps -plibbam-dev
-dh_gencontrol -psamtools
-dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
-dh_md5sums -psamtools
-dh_builddeb -psamtools -- -Z=xz
-dpkg-deb: building package `samtools' in `../samtools_0.1.19-1_s390x.deb'.
-dh_gencontrol -plibbam-dev
-dpkg-gencontrol: warning: Depends field of package libbam-dev: unknown substitution variable ${shlibs:Depends}
-dh_md5sums -plibbam-dev
-dh_builddeb -plibbam-dev -- -Z=xz
-dpkg-deb: building package `libbam-dev' in `../libbam-dev_0.1.19-1_s390x.deb'.
- dpkg-genchanges -B -ms390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org> >../samtools_0.1.19-1_s390x.changes
-dpkg-genchanges: arch-specific upload - not including arch-independent packages
-dpkg-genchanges: binary-only upload - not including any source code
- dpkg-source --after-build samtools-0.1.19
-dpkg-buildpackage: binary only upload (no source included)
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0917
-
-samtools_0.1.19-1_s390x.changes:
-Format: 1.8
-Date: Sat, 30 Mar 2013 17:31:47 +0900
-Source: samtools
-Binary: samtools libbam-dev
-Architecture: s390x
-Version: 0.1.19-1
-Distribution: sid
-Urgency: low
-Maintainer: s390/s390x Build Daemon (zemlinsky) <buildd_s390x-zemlinsky at buildd.debian.org>
-Changed-By: Charles Plessy <plessy at debian.org>
-Description:
- libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format
- samtools - processing sequence alignments in SAM and BAM formats
-Changes:
- samtools (0.1.19-1) unstable; urgency=low
- .
- cb9bd50 Imported https://github.com/samtools/samtools/archive/0.1.19.tar.gz
- 1e6d442 new tools ace2sam, bamcheck, plot-bamcheck, r2plot.lua, vcfutils.lua.
- 2f2d5c5 debian/copyright: collapsed copyright notices from main holders.
- e194f9e Removed fix_float_tag.patch, corrected upstream.
- 9c0e543 Refreshed patches.
- 3e7e0ec Renamed no-pileup-tests.patch fix_example_makefile.patch.
- 8d8550e example/Makefile: pass -lpthread when compiling calDepth.
- fc32243 harden by concatenating Debian's LDFLAGS and CPPFLAGS in CFLAGS.
- 6f75b48 debian/control: normalised with cme.
- e13bb5e debian/control: normalised VCS URLs.
- a1b1b00 debian/control: deleted DM-Upload-Allowed field.
- ddcd54e Use NEWS as upstream changelog.
- 81ad760 Conforms to Policy version 3.9.4.
-Checksums-Sha1:
- 44b0ad7015c66de7ea61172247a7884218c5b8aa 560790 samtools_0.1.19-1_s390x.deb
- 884eb297e57fc14d47b73d4655e291f6fc9ff0c3 122144 libbam-dev_0.1.19-1_s390x.deb
-Checksums-Sha256:
- 8764098ec4269510b9054964c3ca0ebff7c1324ece301d60f210457d23150f54 560790 samtools_0.1.19-1_s390x.deb
- 3afb93b0941f94245f8f25c53d68d10cd5d425e46769655e1a396442e4afc034 122144 libbam-dev_0.1.19-1_s390x.deb
-Files:
- 13d6e54829d787f92d2d384d1febce1e 560790 science optional samtools_0.1.19-1_s390x.deb
- af7829858681083a1704e14e55263cd6 122144 libdevel optional libbam-dev_0.1.19-1_s390x.deb
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Package contents │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-samtools_0.1.19-1_s390x.deb
-───────────────────────────
-
- new debian package, version 2.0.
- size 560790 bytes: control archive= 1937 bytes.
- 32 bytes, 1 lines conffiles
- 793 bytes, 16 lines control
- 2766 bytes, 42 lines md5sums
- Package: samtools
- Version: 0.1.19-1
- Architecture: s390x
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 1452
- Depends: libc6 (>= 2.13), libncurses5 (>= 5.5-5~), libtinfo5, zlib1g (>= 1:1.2.3.3)
- Suggests: python
- Section: science
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- 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
- 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 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/
--rw-r--r-- root/root 1966 2013-03-30 09:17 ./usr/share/doc/samtools/README.bcftools
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/samtools/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/samtools/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/samtools/copyright
--rw-r--r-- root/root 1031 2012-01-09 02:59 ./usr/share/doc/samtools/README.Debian
--rw-r--r-- root/root 592 2012-01-09 02:59 ./usr/share/doc/samtools/reference
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/samtools/NEWS.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/samtools/examples/
--rw-r--r-- root/root 98 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.fa
--rw-r--r-- root/root 886 2013-03-18 14:43 ./usr/share/doc/samtools/examples/00README.txt
--rw-r--r-- root/root 114565 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.sam.gz
--rw-r--r-- root/root 786 2013-03-18 14:43 ./usr/share/doc/samtools/examples/toy.sam
--rw-r--r-- root/root 126580 2013-03-30 09:17 ./usr/share/doc/samtools/examples/ex1.bam
--rw-r--r-- root/root 3225 2013-03-18 14:43 ./usr/share/doc/samtools/examples/ex1.fa
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/samtools/
--rwxr-xr-x root/root 14299 2013-03-18 14:43 ./usr/share/samtools/samtools.pl
--rwxr-xr-x root/root 2112 2013-03-18 14:43 ./usr/share/samtools/bowtie2sam.pl
--rwxr-xr-x root/root 7881 2013-03-18 14:43 ./usr/share/samtools/sam2vcf.pl
--rwxr-xr-x root/root 2415 2013-03-18 14:43 ./usr/share/samtools/blast2sam.pl
--rwxr-xr-x root/root 2729 2013-03-18 14:43 ./usr/share/samtools/wgsim_eval.pl
--rwxr-xr-x root/root 29649 2013-03-18 14:43 ./usr/share/samtools/plot-bamcheck
--rwxr-xr-x root/root 15707 2013-03-18 14:43 ./usr/share/samtools/vcfutils.pl
--rwxr-xr-x root/root 2022 2013-03-18 14:43 ./usr/share/samtools/psl2sam.pl
--rwxr-xr-x root/root 2397 2013-03-18 14:43 ./usr/share/samtools/zoom2sam.pl
--rwxr-xr-x root/root 5778 2013-03-30 09:17 ./usr/share/samtools/varfilter.py
--rwxr-xr-x root/root 5989 2013-03-18 14:43 ./usr/share/samtools/novo2sam.pl
--rwxr-xr-x root/root 21028 2013-03-18 14:43 ./usr/share/samtools/vcfutils.lua
--rwxr-xr-x root/root 2685 2013-03-18 14:43 ./usr/share/samtools/r2plot.lua
--rwxr-xr-x root/root 4996 2013-03-18 14:43 ./usr/share/samtools/interpolate_sam.pl
--rwxr-xr-x root/root 2696 2013-03-18 14:43 ./usr/share/samtools/soap2sam.pl
--rwxr-xr-x root/root 18572 2013-03-18 14:43 ./usr/share/samtools/export2sam.pl
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/man/man1/
--rw-r--r-- root/root 430 2013-03-30 09:17 ./usr/share/man/man1/razip.1.gz
--rw-r--r-- root/root 10654 2013-03-30 09:17 ./usr/share/man/man1/samtools.1.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/bin/
--rwxr-xr-x root/root 494752 2013-03-30 09:17 ./usr/bin/samtools
--rwxr-xr-x root/root 175256 2013-03-30 09:17 ./usr/bin/bcftools
--rwxr-xr-x root/root 31136 2013-03-30 09:17 ./usr/bin/razip
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/samtools/
--rwxr-xr-x root/root 22768 2013-03-30 09:17 ./usr/lib/samtools/wgsim
--rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-short
--rwxr-xr-x root/root 10272 2013-03-30 09:17 ./usr/lib/samtools/md5sum-lite
--rwxr-xr-x root/root 22656 2013-03-30 09:17 ./usr/lib/samtools/ace2sam
--rwxr-xr-x root/root 14424 2013-03-30 09:17 ./usr/lib/samtools/md5fa
--rwxr-xr-x root/root 201392 2013-03-30 09:17 ./usr/lib/samtools/bamcheck
--rwxr-xr-x root/root 10352 2013-03-30 09:17 ./usr/lib/samtools/maq2sam-long
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./etc/bash_completion.d/
--rw-r--r-- root/root 576 2012-07-26 21:52 ./etc/bash_completion.d/samtools
-lrwxrwxrwx root/root 0 2013-03-30 09:17 ./usr/share/man/man1/bcftools.1.gz -> samtools.1.gz
-
-
-libbam-dev_0.1.19-1_s390x.deb
-─────────────────────────────
-
- new debian package, version 2.0.
- size 122144 bytes: control archive= 924 bytes.
- 712 bytes, 17 lines control
- 715 bytes, 11 lines md5sums
- Package: libbam-dev
- Source: samtools
- Version: 0.1.19-1
- Architecture: s390x
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Installed-Size: 461
- Section: libdevel
- Priority: optional
- Homepage: http://samtools.sourceforge.net
- Description: manipulates nucleotide sequence alignments in BAM or SAM format
- The BAM library provides I/O and various operations on manipulating nucleotide
- sequence alignments in the BAM (Binary Alignment/Mapping) or SAM (Sequence
- Alignment/Map) format. It now supports importing from or exporting to SAM,
- sorting, merging, generating pileup, and quickly retrieval of reads overlapped
- with a specified region.
- .
- This library is part of SAMtools.
-
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/share/doc/libbam-dev/
--rw-r--r-- root/root 2466 2013-03-30 08:32 ./usr/share/doc/libbam-dev/changelog.Debian.gz
--rw-r--r-- root/root 916 2013-03-18 14:43 ./usr/share/doc/libbam-dev/AUTHORS
--rw-r--r-- root/root 5012 2013-03-30 07:03 ./usr/share/doc/libbam-dev/copyright
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/changelog.gz
--rw-r--r-- root/root 10421 2013-03-18 14:43 ./usr/share/doc/libbam-dev/NEWS.gz
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/include/samtools/
--rw-r--r-- root/root 3188 2013-03-18 14:43 ./usr/include/samtools/faidx.h
--rw-r--r-- root/root 2688 2013-03-18 14:43 ./usr/include/samtools/sam.h
--rw-r--r-- root/root 6326 2013-03-18 14:43 ./usr/include/samtools/bgzf.h
--rw-r--r-- root/root 25788 2013-03-18 14:43 ./usr/include/samtools/bam.h
--rw-r--r-- root/root 17815 2013-03-18 14:43 ./usr/include/samtools/khash.h
-drwxr-xr-x root/root 0 2013-03-30 09:17 ./usr/lib/
--rw-r--r-- root/root 349450 2013-03-30 09:17 ./usr/lib/libbam.a
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Finished │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Built successfully
-────────────────────────────────────────────────────────────────────────────────
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Post Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Purging /var/lib/schroot/mount/sid-s390x-sbuild-683aa926-ac15-426d-91c5-f4f101ce8fb3/build/buildd-samtools_0.1.19-1-s390x-JVvJbf
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: s390x
-Build-Space: 15508
-Build-Time: 65
-Distribution: sid
-Install-Time: 15
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 97
-Source-Version: 0.1.19-1
-Space: 15508
-Status: successful
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0917
-Build needed 00:01:37, 15508k disc space
-Signature with key '52DC96B8' requested:
diff --git a/sparc.log b/sparc.log
deleted file mode 100644
index 4140d4f..0000000
--- a/sparc.log
+++ /dev/null
@@ -1,610 +0,0 @@
-From buildd at lebrun.debian.org Sat Mar 30 09:19:52 2013
-Return-path: <buildd at lebrun.debian.org>
-Received: from merikanto.debian.org ([2001:858:2:2:216:35ff:fec4:a49a])
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=merikanto.debian.org,
- EMAIL=hostmaster at merikanto.debian.org (verified)
- by grieg.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1ULrx1-0002vg-Ph
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:51 +0000
-Received: from [2001:b68:ff:5:203:baff:fe59:abad] (helo=lebrun.debian.org)
- from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA,
- CN=lebrun.debian.org, EMAIL=hostmaster at lebrun.debian.org (verified)
- by merikanto.debian.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32)
- (Exim 4.72) (envelope-from <buildd at lebrun.debian.org>)
- id 1ULrx0-0001bZ-R6
- for logs at buildd.debian.org; Sat, 30 Mar 2013 09:19:50 +0000
-Received: from buildd by lebrun.debian.org with local (Exim 4.72)
- (envelope-from <buildd at lebrun.debian.org>)
- id 1ULrwy-0005Aj-VO; Sat, 30 Mar 2013 09:19:49 +0000
-Message-Id: <E1ULrwy-0005Aj-VO at lebrun.debian.org>
-MIME-Version: 1.0
-Content-Transfer-Encoding: binary
-X-Mailer: MIME::Lite 3.027 (F2.77; B3.08; Q3.08)
-Date: Sat, 30 Mar 2013 09:19:48 +0000
-From: buildd on lebrun <buildd at lebrun.debian.org>
-To: logs at buildd.debian.org,buildd-admin at lebrun.debian.org
-Subject: Log for attempted build of samtools_0.1.19-1 on sparc (dist=sid)
-Key-Id: B16CDE7F
-Delivered-To: logs at buildd.debian.org
-
-sbuild (Debian sbuild) 0.61.0 (23 Feb 2011) on lebrun.debian.org
-
-╔══════════════════════════════════════════════════════════════════════════════╗
-║ samtools 0.1.19-1 (sparc) 30 Mar 2013 09:14 ║
-╚══════════════════════════════════════════════════════════════════════════════╝
-
-Package: samtools
-Version: 0.1.19-1
-Source Version: 0.1.19-1
-Architecture: sparc
-Get:1 http://debian.carnet.hr unstable Release.gpg [836 B]
-Get:2 http://incoming.debian.org unstable Release.gpg [836 B]
-Get:3 http://incoming.debian.org buildd-unstable Release.gpg [836 B]
-Get:4 http://debian.carnet.hr unstable Release [235 kB]
-Get:5 http://incoming.debian.org unstable Release [235 kB]
-Get:6 http://debian.carnet.hr unstable/main Sources [6484 kB]
-Get:7 http://incoming.debian.org buildd-unstable Release [109 kB]
-Get:8 http://incoming.debian.org unstable/main Sources [6484 kB]
-Get:9 http://debian.carnet.hr unstable/contrib Sources [51.0 kB]
-Get:10 http://debian.carnet.hr unstable/non-free Sources [101 kB]
-Get:11 http://debian.carnet.hr unstable/main sparc Packages [6115 kB]
-Get:12 http://debian.carnet.hr unstable/contrib sparc Packages [35.6 kB]
-Get:13 http://incoming.debian.org unstable/contrib Sources [51.0 kB]
-Get:14 http://incoming.debian.org unstable/non-free Sources [101 kB]
-Get:15 http://incoming.debian.org unstable/main sparc Packages [6115 kB]
-Get:16 http://incoming.debian.org unstable/contrib sparc Packages [35.6 kB]
-Get:17 http://incoming.debian.org buildd-unstable/main Sources [11.2 kB]
-Get:18 http://incoming.debian.org buildd-unstable/contrib Sources [761 B]
-Get:19 http://incoming.debian.org buildd-unstable/non-free Sources [14 B]
-Get:20 http://incoming.debian.org buildd-unstable/main sparc Packages [12.7 kB]
-Get:21 http://incoming.debian.org buildd-unstable/contrib sparc Packages [14 B]
-Fetched 26.2 MB in 60s (435 kB/s)
-Reading package lists...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Fetch source files │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Check APT
-─────────
-
-Checking available source versions...
-
-Download source files with APT
-──────────────────────────────
-
-Reading package lists...
-Building dependency tree...
-Reading state information...
-NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
-git://anonscm.debian.org/debian-med/samtools.git
-Need to get 570 kB of source archives.
-Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (dsc) [2078 B]
-Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (tar) [558 kB]
-Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 0.1.19-1 (diff) [10.2 kB]
-Fetched 570 kB in 1s (368 kB/s)
-Download complete and in download only mode
-
-Check arch
-──────────
-
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install core build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: build-essential, fakeroot
-Checking for already installed dependencies...
-build-essential: already installed (11.6)
-fakeroot: already installed (1.18.4-2)
-Checking for dependency conflicts...
-Installing positive dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Install samtools build dependencies (internal resolver) │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, libc6-dev-sparc64, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bash-completion, cdbs, quilt, libncurses5-dev, zlib1g-dev
-Checking for already installed dependencies...
-base-files: already installed (7.1)
-base-passwd: already installed (3.5.26)
-bash: already installed (4.2+dfsg-0.1)
-bsdutils: already installed (1:2.20.1-5.3)
-coreutils: already installed (8.13-3.3)
-dash: already installed (0.5.7-3)
-debianutils: already installed (4.3.4)
-diffutils: already installed (1:3.2-8)
-dpkg: already installed (1.16.10)
-e2fsprogs: already installed (1.42.5-1.1)
-findutils: already installed (4.4.2-5)
-grep: already installed (2.14-1)
-gzip: already installed (1.5-1.1)
-hostname: already installed (3.12)
-libc-bin: already installed (2.13-38)
-login: already installed (1:4.1.5.1-1)
-mount: already installed (2.20.1-5.3)
-ncurses-base: already installed (5.9-10)
-ncurses-bin: already installed (5.9-10)
-perl-base: already installed (5.14.2-20)
-sed: already installed (4.2.1-10)
-sysvinit: already installed (2.88dsf-41)
-sysvinit-utils: already installed (2.88dsf-41)
-tar: already installed (1.26+dfsg-0.1)
-util-linux: already installed (2.20.1-5.3)
-libc6-dev: already installed (2.13-38)
-libc6-dev-sparc64: already installed (2.13-38)
-gcc: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-g++: already installed (4:4.6.3-8 >= 4:4.4.3 is satisfied)
-make: already installed (3.81-8.2)
-dpkg-dev: already installed (1.16.10 >= 1.13.5 is satisfied)
-debhelper: missing
-Using default version 9.20120909
-bash-completion: missing
-cdbs: missing
-quilt: missing
-libncurses5-dev: missing
-zlib1g-dev: missing
-Checking for dependency conflicts...
-Installing positive dependencies: debhelper bash-completion cdbs quilt libncurses5-dev zlib1g-dev
-Reading package lists...
-Building dependency tree...
-Reading state information...
-The following extra packages will be installed:
- bsdmainutils diffstat file gettext gettext-base groff-base html2text
- intltool-debian libasprintf-dev libasprintf0c2 libcroco3 libffi5
- libgettextpo-dev libgettextpo0 libglib2.0-0 libmagic1 libpcre3 libpipeline1
- libtinfo-dev libunistring0 libxml2 man-db po-debconf
-Suggested packages:
- wamerican wordlist whois vacation devscripts dh-make gettext-doc groff
- ncurses-doc less www-browser libmail-box-perl procmail graphviz default-mta
- mail-transport-agent
-Recommended packages:
- autotools-dev curl wget lynx-cur autopoint libglib2.0-data shared-mime-info
- xml-core libmail-sendmail-perl
-The following NEW packages will be installed:
- bash-completion bsdmainutils cdbs debhelper diffstat file gettext
- gettext-base groff-base html2text intltool-debian libasprintf-dev
- libasprintf0c2 libcroco3 libffi5 libgettextpo-dev libgettextpo0 libglib2.0-0
- libmagic1 libncurses5-dev libpcre3 libpipeline1 libtinfo-dev libunistring0
- libxml2 man-db po-debconf quilt zlib1g-dev
-0 upgraded, 29 newly installed, 0 to remove and 2 not upgraded.
-Need to get 9825 kB of archives.
-After this operation, 29.1 MB of additional disk space will be used.
-Get:1 http://debian.carnet.hr/debian/ unstable/main libpipeline1 sparc 1.2.2-2 [36.3 kB]
-Get:2 http://debian.carnet.hr/debian/ unstable/main groff-base sparc 1.22.2-1 [693 kB]
-Get:3 http://debian.carnet.hr/debian/ unstable/main bsdmainutils sparc 9.0.4 [203 kB]
-Get:4 http://debian.carnet.hr/debian/ unstable/main man-db sparc 2.6.3-3 [865 kB]
-Get:5 http://debian.carnet.hr/debian/ unstable/main bash-completion all 1:2.0-1 [193 kB]
-Get:6 http://debian.carnet.hr/debian/ unstable/main libasprintf0c2 sparc 0.18.1.1-10 [26.9 kB]
-Get:7 http://debian.carnet.hr/debian/ unstable/main libmagic1 sparc 1:5.11-2.1 [197 kB]
-Get:8 http://debian.carnet.hr/debian/ unstable/main libpcre3 sparc 1:8.31-2 [252 kB]
-Get:9 http://debian.carnet.hr/debian/ unstable/main libxml2 sparc 2.8.0+dfsg1-7+nmu1 [826 kB]
-Get:10 http://debian.carnet.hr/debian/ unstable/main libffi5 sparc 3.0.10-3 [22.7 kB]
-Get:11 http://debian.carnet.hr/debian/ unstable/main libglib2.0-0 sparc 2.33.12+really2.32.4-5 [1645 kB]
-Get:12 http://debian.carnet.hr/debian/ unstable/main libcroco3 sparc 0.6.6-2 [114 kB]
-Get:13 http://debian.carnet.hr/debian/ unstable/main libunistring0 sparc 0.9.3-5 [416 kB]
-Get:14 http://debian.carnet.hr/debian/ unstable/main libgettextpo0 sparc 0.18.1.1-10 [130 kB]
-Get:15 http://debian.carnet.hr/debian/ unstable/main file sparc 1:5.11-2.1 [51.1 kB]
-Get:16 http://debian.carnet.hr/debian/ unstable/main gettext-base sparc 0.18.1.1-10 [148 kB]
-Get:17 http://debian.carnet.hr/debian/ unstable/main cdbs all 0.4.120 [80.4 kB]
-Get:18 http://debian.carnet.hr/debian/ unstable/main html2text sparc 1.3.2a-15 [100 kB]
-Get:19 http://debian.carnet.hr/debian/ unstable/main libasprintf-dev sparc 0.18.1.1-10 [26.6 kB]
-Get:20 http://debian.carnet.hr/debian/ unstable/main libgettextpo-dev sparc 0.18.1.1-10 [172 kB]
-Get:21 http://debian.carnet.hr/debian/ unstable/main gettext sparc 0.18.1.1-10 [1745 kB]
-Get:22 http://debian.carnet.hr/debian/ unstable/main intltool-debian all 0.35.0+20060710.1 [30.8 kB]
-Get:23 http://debian.carnet.hr/debian/ unstable/main po-debconf all 1.0.16+nmu2 [224 kB]
-Get:24 http://debian.carnet.hr/debian/ unstable/main debhelper all 9.20120909 [705 kB]
-Get:25 http://debian.carnet.hr/debian/ unstable/main diffstat sparc 1.55-3 [28.6 kB]
-Get:26 http://debian.carnet.hr/debian/ unstable/main libtinfo-dev sparc 5.9-10 [97.5 kB]
-Get:27 http://debian.carnet.hr/debian/ unstable/main libncurses5-dev sparc 5.9-10 [204 kB]
-Get:28 http://debian.carnet.hr/debian/ unstable/main quilt all 0.60-8 [381 kB]
-Get:29 http://debian.carnet.hr/debian/ unstable/main zlib1g-dev sparc 1:1.2.7.dfsg-13 [211 kB]
-debconf: delaying package configuration, since apt-utils is not installed
-Fetched 9825 kB in 14s (659 kB/s)
-Selecting previously unselected package libpipeline1:sparc.
-(Reading database ... 11151 files and directories currently installed.)
-Unpacking libpipeline1:sparc (from .../libpipeline1_1.2.2-2_sparc.deb) ...
-Selecting previously unselected package groff-base.
-Unpacking groff-base (from .../groff-base_1.22.2-1_sparc.deb) ...
-Selecting previously unselected package bsdmainutils.
-Unpacking bsdmainutils (from .../bsdmainutils_9.0.4_sparc.deb) ...
-Selecting previously unselected package man-db.
-Unpacking man-db (from .../man-db_2.6.3-3_sparc.deb) ...
-Selecting previously unselected package bash-completion.
-Unpacking bash-completion (from .../bash-completion_1%3a2.0-1_all.deb) ...
-Selecting previously unselected package libasprintf0c2:sparc.
-Unpacking libasprintf0c2:sparc (from .../libasprintf0c2_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package libmagic1:sparc.
-Unpacking libmagic1:sparc (from .../libmagic1_1%3a5.11-2.1_sparc.deb) ...
-Selecting previously unselected package libpcre3:sparc.
-Unpacking libpcre3:sparc (from .../libpcre3_1%3a8.31-2_sparc.deb) ...
-Selecting previously unselected package libxml2:sparc.
-Unpacking libxml2:sparc (from .../libxml2_2.8.0+dfsg1-7+nmu1_sparc.deb) ...
-Selecting previously unselected package libffi5:sparc.
-Unpacking libffi5:sparc (from .../libffi5_3.0.10-3_sparc.deb) ...
-Selecting previously unselected package libglib2.0-0:sparc.
-Unpacking libglib2.0-0:sparc (from .../libglib2.0-0_2.33.12+really2.32.4-5_sparc.deb) ...
-Selecting previously unselected package libcroco3:sparc.
-Unpacking libcroco3:sparc (from .../libcroco3_0.6.6-2_sparc.deb) ...
-Selecting previously unselected package libunistring0:sparc.
-Unpacking libunistring0:sparc (from .../libunistring0_0.9.3-5_sparc.deb) ...
-Selecting previously unselected package libgettextpo0:sparc.
-Unpacking libgettextpo0:sparc (from .../libgettextpo0_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package file.
-Unpacking file (from .../file_1%3a5.11-2.1_sparc.deb) ...
-Selecting previously unselected package gettext-base.
-Unpacking gettext-base (from .../gettext-base_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package cdbs.
-Unpacking cdbs (from .../archives/cdbs_0.4.120_all.deb) ...
-Selecting previously unselected package html2text.
-Unpacking html2text (from .../html2text_1.3.2a-15_sparc.deb) ...
-Selecting previously unselected package libasprintf-dev:sparc.
-Unpacking libasprintf-dev:sparc (from .../libasprintf-dev_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package libgettextpo-dev:sparc.
-Unpacking libgettextpo-dev:sparc (from .../libgettextpo-dev_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package gettext.
-Unpacking gettext (from .../gettext_0.18.1.1-10_sparc.deb) ...
-Selecting previously unselected package intltool-debian.
-Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
-Selecting previously unselected package po-debconf.
-Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
-Selecting previously unselected package debhelper.
-Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
-Selecting previously unselected package diffstat.
-Unpacking diffstat (from .../diffstat_1.55-3_sparc.deb) ...
-Selecting previously unselected package libtinfo-dev:sparc.
-Unpacking libtinfo-dev:sparc (from .../libtinfo-dev_5.9-10_sparc.deb) ...
-Selecting previously unselected package libncurses5-dev.
-Unpacking libncurses5-dev (from .../libncurses5-dev_5.9-10_sparc.deb) ...
-Selecting previously unselected package quilt.
-Unpacking quilt (from .../archives/quilt_0.60-8_all.deb) ...
-Selecting previously unselected package zlib1g-dev:sparc.
-Unpacking zlib1g-dev:sparc (from .../zlib1g-dev_1%3a1.2.7.dfsg-13_sparc.deb) ...
-Setting up libpipeline1:sparc (1.2.2-2) ...
-Setting up groff-base (1.22.2-1) ...
-Setting up bsdmainutils (9.0.4) ...
-update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
-update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
-Setting up man-db (2.6.3-3) ...
-Building database of manual pages ...
-Setting up bash-completion (1:2.0-1) ...
-Setting up libasprintf0c2:sparc (0.18.1.1-10) ...
-Setting up libmagic1:sparc (1:5.11-2.1) ...
-Setting up libpcre3:sparc (1:8.31-2) ...
-Setting up libxml2:sparc (2.8.0+dfsg1-7+nmu1) ...
-Setting up libffi5:sparc (3.0.10-3) ...
-Setting up libglib2.0-0:sparc (2.33.12+really2.32.4-5) ...
-No schema files found: doing nothing.
-Setting up libcroco3:sparc (0.6.6-2) ...
-Setting up libunistring0:sparc (0.9.3-5) ...
-Setting up libgettextpo0:sparc (0.18.1.1-10) ...
-Setting up file (1:5.11-2.1) ...
-Setting up gettext-base (0.18.1.1-10) ...
-Setting up cdbs (0.4.120) ...
-Setting up html2text (1.3.2a-15) ...
-Setting up libasprintf-dev:sparc (0.18.1.1-10) ...
-Setting up libgettextpo-dev:sparc (0.18.1.1-10) ...
-Setting up gettext (0.18.1.1-10) ...
-Setting up intltool-debian (0.35.0+20060710.1) ...
-Setting up po-debconf (1.0.16+nmu2) ...
-Setting up debhelper (9.20120909) ...
-Setting up diffstat (1.55-3) ...
-Setting up libtinfo-dev:sparc (5.9-10) ...
-Setting up libncurses5-dev (5.9-10) ...
-Setting up quilt (0.60-8) ...
-Setting up zlib1g-dev:sparc (1:1.2.7.dfsg-13) ...
-Removing negative dependencies:
-Reading package lists...
-Building dependency tree...
-Reading state information...
-0 upgraded, 0 newly installed, 0 to remove and 2 not upgraded.
-Checking correctness of dependencies...
-Kernel: Linux 2.6.32-5-sparc64-smp sparc (sparc64)
-Toolchain package versions: binutils_2.22-8 dpkg-dev_1.16.10 g++-4.6_4.6.3-15 gcc-4.6_4.6.3-15 libc6-dev_2.13-38 libstdc++6_4.7.2-5 libstdc++6-4.6-dev_4.6.3-15 linux-libc-dev_3.2.39-2
-Package versions: apt_0.9.7.8 base-files_7.1 base-passwd_3.5.26 bash_4.2+dfsg-0.1 bash-completion_1:2.0-1 binutils_2.22-8 bsdmainutils_9.0.4 bsdutils_1:2.20.1-5.3 build-essential_11.6 bzip2_1.0.6-4 cdbs_0.4.120 coreutils_8.13-3.3 cpp_4:4.6.3-8 cpp-4.6_4.6.3-15 dash_0.5.7-3 debconf_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debian-archive-keyring_2012.4 debianutils_4.3.4 diffstat_1.55-3 diffutils_1:3.2-8 dpkg_1.16.10 dpkg-dev_1.16.10 e2fslibs_1.42.5-1.1 e2fsprogs_1.42.5-1.1 fakeroot_1. [...]
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Build │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-
-Unpack source
-─────────────
-
-gpgv: keyblock resource `/home/buildd/.gnupg/trustedkeys.gpg': file open error
-gpgv: Signature made Sat Mar 30 08:51:24 2013 UTC using RSA key ID 2295D502
-gpgv: Can't check signature: public key not found
-dpkg-source: warning: failed to verify signature on ./samtools_0.1.19-1.dsc
-dpkg-source: info: extracting samtools in samtools-0.1.19
-dpkg-source: info: unpacking samtools_0.1.19.orig.tar.gz
-dpkg-source: info: unpacking samtools_0.1.19-1.debian.tar.gz
-dpkg-source: info: applying fix_example_makefile.patch
-dpkg-source: info: applying fix_segfault_with_small_ref.patch
-dpkg-source: info: applying fix_coverage_cap.patch
-
-Check disc space
-────────────────
-
-
-dpkg-buildpackage
-─────────────────
-
-dpkg-buildpackage: source package samtools
-dpkg-buildpackage: source version 0.1.19-1
- dpkg-source --before-build samtools-0.1.19
-dpkg-buildpackage: host architecture sparc
- fakeroot debian/rules clean
-test -x debian/rules
-dh_testroot
-rm -f debian/stamp-makefile-build debian/stamp-makefile-install
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -k clean
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip samtools *~ *.a *.so.* *.so *.dylib
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-rm -fr gmon.out *.o a.out *.dSYM bcftools *~ *.a bcf.aux bcf.log bcf.pdf *.class libbcf.*.dylib libbcf.so*
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-rm -fr gmon.out *.o a.out *.exe *.dSYM md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck *~ *.a
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-rm -f debian/stamp-makefile-check
-dh_clean
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-if [ -d "." ]; then \
- cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null pop -a -R || test $? = 2 ; \
- fi
-Removing patch fix_coverage_cap.patch
-Restoring bam2depth.c
-
-Removing patch fix_segfault_with_small_ref.patch
-Restoring bam_plcmd.c
-
-Removing patch fix_example_makefile.patch
-Restoring examples/Makefile
-
-No patches applied
-rm -rf ./.pc
-rm -f debian/stamp-patch*
-rm -f examples/calDepth examples/ex1.bam examples/ex1.bam.bai examples/ex1.fa.fai examples/ex1.glf examples/ex1.glfview.gz examples/ex1.pileup.gz examples/ex1a.bam examples/ex1b.bam examples/ex1f-rmduppe.bam examples/ex1f-rmdupse.bam examples/ex1f.bam examples/ex1f.rg examples/ex1.bcf
- debian/rules build-arch
-test -x debian/rules
-mkdir -p "."
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_DH_BUILDDEB_ARGS is a deprecated variable
-/usr/share/cdbs/1/rules/buildcore.mk:109: WARNING: DEB_COMPRESS_EXCLUDE is a deprecated variable
-/usr/bin/make -f debian/rules reverse-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[1]: Nothing to be done for `reverse-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-cd . && QUILT_PATCHES=/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/debian/patches quilt --quiltrc /dev/null push -a || test $? = 2
-Applying patch fix_example_makefile.patch
-patching file examples/Makefile
-
-Applying patch fix_segfault_with_small_ref.patch
-patching file bam_plcmd.c
-
-Applying patch fix_coverage_cap.patch
-patching file bam2depth.c
-
-Now at patch fix_coverage_cap.patch
-touch debian/stamp-patched
-/usr/bin/make -f debian/rules update-config
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[1]: Nothing to be done for `update-config'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" all all-recur razip lib
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
-bgzf.c: In function 'worker_aux':
-bgzf.c:392:9: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
-bgzf.c: In function 'bgzf_close':
-bgzf.c:572:11: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
-bam_import.c: In function 'append_text':
-bam_import.c:179:13: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint32_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-bam_import.c:186:9: warning: format '%ld' expects argument of type 'long int', but argument 6 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
-bam_index.c: In function 'bam_index_load_core':
-bam_index.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:342:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:355:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:358:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:362:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:366:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:376:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-bam_index.c:380:8: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
-bam_pileup.c: In function 'resolve_cigar2':
-bam_pileup.c:75:9: warning: variable 'is_head' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o
-razf.c: In function 'razf_close':
-razf.c:804:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:805:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:808:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:810:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_end_flush':
-razf.c:258:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function '_razf_write':
-razf.c:201:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'save_zindex':
-razf.c:96:17: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:99:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:106:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:107:7: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c: In function 'razf_flush':
-razf.c:221:8: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razf.c:234:9: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
-knetfile.c: In function 'khttp_connect_file':
-knetfile.c:415:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-knetfile.c: In function 'kftp_send_cmd':
-knetfile.c:236:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
-bam_reheader.c: In function 'bam_reheader':
-bam_reheader.c:12:16: warning: variable 'old' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
-kprobaln.c: In function 'kpa_glocal':
-kprobaln.c:78:21: warning: variable 'is_diff' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
-ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
-bcf.c: In function 'bcf_fmt_core':
-bcf.c:233:9: warning: variable 'iPL' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
-bcfutils.c: In function 'bcf_fit_alt':
-bcfutils.c:119:9: warning: variable 'ipl' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
-em.c: In function 'bcf_em1':
-em.c:174:12: warning: variable 'n2' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
-ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-make[2]: Nothing to be done for `lib'.
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
-cut_target.c: In function 'main_cut_target':
-cut_target.c:137:36: warning: variable 'lastpos' set but not used [-Wunused-but-set-variable]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o
-padding.c: In function 'bam_pad2unpad':
-padding.c:173:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'size_t' [-Wformat]
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_html.c -o bam_tview_html.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-make[3]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-make[3]: Nothing to be done for `lib'.
-make[3]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o bam_tview_curses.o bam_tview_html.o -Wl,-z,relro libbam.a -Lbcftools -lbcf -lcurses -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. call1.c -o call1.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. main.c -o main.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o ../bedidx.o -L. -lbcf -lm -lz -lpthread
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/bcftools'
-make[2]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -o md5sum-lite.o md5.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5sum-lite md5sum-lite.o
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. md5.c -o md5.o
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o md5fa.o md5fa.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o md5fa md5.o md5fa.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o maq2sam-short maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -o maq2sam-long maq2sam.c -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o ace2sam.o ace2sam.c
-ace2sam.c: In function 'main':
-ace2sam.c:112:4: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t' [-Wformat]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o ace2sam ace2sam.o -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o wgsim.o wgsim.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o wgsim wgsim.o -lm -lz
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -c -I.. -o bamcheck.o bamcheck.c
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o bamcheck bamcheck.o -L.. -lm -lbam -lpthread -lz
-make[2]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/misc'
-gcc -c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razip.c -o razip.o
-razip.c: In function 'main':
-razip.c:131:10: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
-razip.c: In function 'write_open':
-razip.c:32:9: warning: ignoring return value of 'scanf', declared with attribute warn_unused_result [-Wunused-result]
-gcc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2 -o razip razip.o razf.o knetfile.o -lz
-make[1]: Nothing to be done for `lib'.
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19'
-touch debian/stamp-makefile-build
-/usr/bin/make -C . CFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -fPIC -Wl,-z,relro -D_FORTIFY_SOURCE=2" CXXFLAGS="-g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall" CPPFLAGS="-D_FORTIFY_SOURCE=2" LDFLAGS="-Wl,-z,relro" -C examples all
-make[1]: Entering directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/examples'
-../samtools faidx ex1.fa
-../samtools import ex1.fa.fai ex1.sam.gz ex1.bam
-[sam_header_read2] 2 sequences loaded.
-make[1]: *** [ex1.bam] Bus error
-make[1]: *** Deleting file `ex1.bam'
-make[1]: Leaving directory `/build/buildd-samtools_0.1.19-1-sparc-XTmM23/samtools-0.1.19/examples'
-make: *** [debian/stamp-makefile-check] Error 2
-dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
-────────────────────────────────────────────────────────────────────────────────
-Build finished at 20130330-0919
-FAILED [dpkg-buildpackage died]
-────────────────────────────────────────────────────────────────────────────────
-Purging /var/lib/schroot/mount/sid-sparc-sbuild-a9e2fc50-8623-4453-ba1c-9450161e0f4b/build/buildd-samtools_0.1.19-1-sparc-XTmM23
-Not cleaning session: cloned chroot in use
-
-┌──────────────────────────────────────────────────────────────────────────────┐
-│ Summary │
-└──────────────────────────────────────────────────────────────────────────────┘
-
-Architecture: sparc
-Build-Space: 8216
-Build-Time: 151
-Distribution: sid
-Fail-Stage: build
-Install-Time: 85
-Job: samtools_0.1.19-1
-Package: samtools
-Package-Time: 319
-Source-Version: 0.1.19-1
-Space: 8216
-Status: attempted
-Version: 0.1.19-1
-────────────────────────────────────────────────────────────────────────────────
-Finished at 20130330-0919
-Build needed 00:05:19, 8216k disc space
diff --git a/x32.log b/x32.log
new file mode 100644
index 0000000..9e4d453
--- /dev/null
+++ b/x32.log
@@ -0,0 +1,768 @@
+
+sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on vs76.physik.fu-berlin.de
+
+╔══════════════════════════════════════════════════════════════════════════════╗
+║ samtools 1.2-3 (x32) 22 Sep 2015 18:49 ║
+╚══════════════════════════════════════════════════════════════════════════════╝
+
+Package: samtools
+Version: 1.2-3
+Source Version: 1.2-3
+Distribution: sid
+Machine Architecture: amd64
+Host Architecture: x32
+Build Architecture: x32
+
+I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY/samtools-1.2' with '«PKGBUILDDIR»'
+I: NOTICE: Log filtering will replace 'build/samtools-9mkKnY' with '«BUILDDIR»'
+I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7' with '«CHROOT»'
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Update chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Get:1 http://ftp.debian.org unstable InRelease [253 kB]
+Get:2 http://incoming.debian.org buildd-unstable InRelease [111 kB]
+Get:3 http://incoming.debian.org buildd-unstable/main Sources [353 kB]
+Get:4 http://ftp.debian.org unstable/main Sources/DiffIndex [7876 B]
+Get:5 http://ftp.debian-ports.org unstable InRelease [41.0 kB]
+Ign http://incoming.debian-ports.org unstable InRelease
+Get:6 http://ftp.debian.org unstable/main 2015-09-17-1433.22.pdiff [18.3 kB]
+Get:7 http://ftp.debian.org unstable/main 2015-09-17-2033.47.pdiff [17.0 kB]
+Get:8 http://ftp.debian.org unstable/main 2015-09-18-0236.10.pdiff [2554 B]
+Get:9 http://ftp.debian.org unstable/main 2015-09-18-0836.19.pdiff [3115 B]
+Get:10 http://ftp.debian.org unstable/main 2015-09-18-1434.45.pdiff [20.1 kB]
+Get:11 http://incoming.debian-ports.org unstable Release.gpg [836 B]
+Get:12 http://ftp.debian.org unstable/main 2015-09-18-2038.10.pdiff [8273 B]
+Get:13 http://ftp.debian.org unstable/main 2015-09-19-0234.31.pdiff [15.8 kB]
+Get:14 http://ftp.debian-ports.org unreleased InRelease [44.8 kB]
+Get:15 http://ftp.debian.org unstable/main 2015-09-19-0836.28.pdiff [5086 B]
+Get:16 http://ftp.debian.org unstable/main 2015-09-19-1440.27.pdiff [12.2 kB]
+Get:17 http://ftp.debian.org unstable/main 2015-09-19-2034.22.pdiff [28.8 kB]
+Get:18 http://ftp.debian.org unstable/main 2015-09-20-0235.43.pdiff [10.9 kB]
+Get:19 http://incoming.debian-ports.org unstable Release [39.6 kB]
+Get:20 http://ftp.debian.org unstable/main 2015-09-20-0846.24.pdiff [2176 B]
+Get:21 http://ftp.debian.org unstable/main 2015-09-20-1435.54.pdiff [11.3 kB]
+Get:22 http://ftp.debian.org unstable/main 2015-09-20-2047.32.pdiff [10.4 kB]
+Get:23 http://ftp.debian.org unstable/main 2015-09-21-0236.32.pdiff [8959 B]
+Get:24 http://ftp.debian.org unstable/main 2015-09-21-0835.50.pdiff [4865 B]
+Get:25 http://ftp.debian.org unstable/main 2015-09-21-1436.46.pdiff [17.2 kB]
+Get:26 http://ftp.debian.org unstable/main 2015-09-21-2043.02.pdiff [12.8 kB]
+Get:27 http://ftp.debian-ports.org unstable/main x32 Packages [13.0 MB]
+Get:28 http://ftp.debian.org unstable/main 2015-09-22-0237.33.pdiff [10.4 kB]
+Get:29 http://ftp.debian.org unstable/main 2015-09-22-0834.54.pdiff [6855 B]
+Get:30 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
+Get:31 http://ftp.debian.org unstable/main 2015-09-22-1435.11.pdiff [15.1 kB]
+Get:32 http://incoming.debian-ports.org unstable/main x32 Packages [36.7 kB]
+Ign http://incoming.debian-ports.org unstable/main Translation-en
+Get:33 http://ftp.debian-ports.org unreleased/main x32 Packages [63.0 kB]
+Ign http://ftp.debian-ports.org unstable/main Translation-en
+Ign http://ftp.debian-ports.org unreleased/main Translation-en
+Fetched 14.2 MB in 10s (1346 kB/s)
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Fetch source files │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Check APT
+─────────
+
+Checking available source versions...
+
+Download source files with APT
+──────────────────────────────
+
+Reading package lists...
+Building dependency tree...
+Reading state information...
+NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
+git://anonscm.debian.org/debian-med/samtools.git
+Need to get 4330 kB of source archives.
+Get:1 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (dsc) [2117 B]
+Get:2 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (tar) [4319 kB]
+Get:3 http://incoming.debian.org/debian-buildd/ buildd-unstable/main samtools 1.2-3 (diff) [9680 B]
+Fetched 4330 kB in 2s (1775 kB/s)
+Download complete and in download only mode
+
+Check architectures
+───────────────────
+
+
+Check dependencies
+──────────────────
+
+Merged Build-Depends: build-essential, fakeroot
+Filtered Build-Depends: build-essential, fakeroot
+dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ba45YF/apt_archive/sbuild-build-depends-core-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install core build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ fakeroot libfakeroot
+The following NEW packages will be installed:
+ fakeroot libfakeroot sbuild-build-depends-core-dummy
+0 upgraded, 3 newly installed, 0 to remove and 24 not upgraded.
+Need to get 129 kB/130 kB of archives.
+After this operation, 411 kB of additional disk space will be used.
+Get:1 http://ftp.debian-ports.org/debian/ unstable/main libfakeroot x32 1.20.2-1 [44.8 kB]
+Get:2 http://ftp.debian-ports.org/debian/ unstable/main fakeroot x32 1.20.2-1 [84.6 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 129 kB in 1s (115 kB/s)
+Selecting previously unselected package libfakeroot:x32.
+(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 12802 files and directories currently installed.)
+Preparing to unpack .../libfakeroot_1.20.2-1_x32.deb ...
+Unpacking libfakeroot:x32 (1.20.2-1) ...
+Selecting previously unselected package fakeroot.
+Preparing to unpack .../fakeroot_1.20.2-1_x32.deb ...
+Unpacking fakeroot (1.20.2-1) ...
+Selecting previously unselected package sbuild-build-depends-core-dummy.
+Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
+Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
+Setting up libfakeroot:x32 (1.20.2-1) ...
+Setting up 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) ...
+Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), zlib1g-dev, tabix (>= 1.0)
+dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/«BUILDDIR»/resolver-7knP0Q/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
+OK
+Ign file: ./ InRelease
+Get:1 file: ./ Release.gpg [299 B]
+Get:2 file: ./ Release [2119 B]
+Ign file: ./ Translation-en
+Reading package lists...
+Reading package lists...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Install samtools build dependencies (apt-based resolver) │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Installing build dependencies
+Reading package lists...
+Building dependency tree...
+Reading state information...
+The following extra packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf tabix zlib1g-dev
+Suggested packages:
+ wamerican wordlist whois vacation dh-make gettext-doc autopoint
+ libasprintf-dev libgettextpo-dev groff ncurses-doc less www-browser
+ libmail-box-perl
+Recommended packages:
+ curl wget lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs xml-core
+ libmail-sendmail-perl
+The following NEW packages will be installed:
+ bash-completion bsdmainutils debhelper file gettext gettext-base groff-base
+ intltool-debian libcroco3 libffi6 libglib2.0-0 libhts-dev libhts1 libicu55
+ libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
+ libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
+ tabix zlib1g-dev
+0 upgraded, 26 newly installed, 0 to remove and 24 not upgraded.
+Need to get 18.3 MB/18.3 MB of archives.
+After this operation, 64.0 MB of additional disk space will be used.
+Get:1 http://ftp.debian-ports.org/debian/ unstable/main bash-completion all 1:2.1-4.2 [179 kB]
+Get:2 http://ftp.debian-ports.org/debian/ unstable/main groff-base x32 1.22.3-1 [1199 kB]
+Get:3 http://ftp.debian-ports.org/debian/ unstable/main bsdmainutils x32 9.0.6 [183 kB]
+Get:4 http://ftp.debian-ports.org/debian/ unstable/main libpipeline1 x32 1.4.1-1 [28.0 kB]
+Get:5 http://ftp.debian-ports.org/debian/ unstable/main man-db x32 2.7.3-1 [1003 kB]
+Get:6 http://ftp.debian-ports.org/debian/ unstable/main libffi6 x32 3.2.1-3 [19.9 kB]
+Get:7 http://ftp.debian-ports.org/debian/ unstable/main libunistring0 x32 0.9.3-5.2 [289 kB]
+Get:8 http://ftp.debian-ports.org/debian/ unstable/main libmagic1 x32 1:5.25-1 [256 kB]
+Get:9 http://ftp.debian-ports.org/debian/ unstable/main file x32 1:5.25-1 [61.5 kB]
+Get:10 http://ftp.debian-ports.org/debian/ unstable/main gettext-base x32 0.19.6-1 [123 kB]
+Get:11 http://ftp.debian-ports.org/debian/ unstable/main libicu55 x32 55.1-5 [7659 kB]
+Get:12 http://ftp.debian-ports.org/debian/ unstable/main libxml2 x32 2.9.2+zdfsg1-4 [924 kB]
+Get:13 http://ftp.debian-ports.org/debian/ unstable/main libglib2.0-0 x32 2.44.1-1.1 [2471 kB]
+Get:14 http://ftp.debian-ports.org/debian/ unstable/main libcroco3 x32 0.6.8-3+b1 [135 kB]
+Get:15 http://ftp.debian-ports.org/debian/ unstable/main gettext x32 0.19.6-1 [1466 kB]
+Get:16 http://ftp.debian-ports.org/debian/ unstable/main intltool-debian all 0.35.0+20060710.4 [26.3 kB]
+Get:17 http://ftp.debian-ports.org/debian/ unstable/main po-debconf all 1.0.18 [248 kB]
+Get:18 http://ftp.debian-ports.org/debian/ unstable/main debhelper all 9.20150811 [817 kB]
+Get:19 http://ftp.debian-ports.org/debian/ unstable/main libhts1 x32 1.2.1-1 [226 kB]
+Get:20 http://ftp.debian-ports.org/debian/ unstable/main libhts-dev x32 1.2.1-1 [274 kB]
+Get:21 http://ftp.debian-ports.org/debian/ unstable/main libio-pty-perl x32 1:1.08-1+b2 [36.0 kB]
+Get:22 http://ftp.debian-ports.org/debian/ unstable/main libtinfo-dev x32 6.0+20150810-1 [76.5 kB]
+Get:23 http://ftp.debian-ports.org/debian/ unstable/main libncurses5-dev x32 6.0+20150810-1 [170 kB]
+Get:24 http://ftp.debian-ports.org/debian/ unstable/main tabix x32 1.2.1-1 [221 kB]
+Get:25 http://ftp.debian-ports.org/debian/ unstable/main zlib1g-dev x32 1:1.2.8.dfsg-2+b1 [206 kB]
+debconf: delaying package configuration, since apt-utils is not installed
+Fetched 18.3 MB in 10s (1822 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%
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(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 ... 12852 files and directories currently installed.)
+Preparing to unpack .../bash-completion_1%3a2.1-4.2_all.deb ...
+Unpacking bash-completion (1:2.1-4.2) ...
+Selecting previously unselected package groff-base.
+Preparing to unpack .../groff-base_1.22.3-1_x32.deb ...
+Unpacking groff-base (1.22.3-1) ...
+Selecting previously unselected package bsdmainutils.
+Preparing to unpack .../bsdmainutils_9.0.6_x32.deb ...
+Unpacking bsdmainutils (9.0.6) ...
+Selecting previously unselected package libpipeline1:x32.
+Preparing to unpack .../libpipeline1_1.4.1-1_x32.deb ...
+Unpacking libpipeline1:x32 (1.4.1-1) ...
+Selecting previously unselected package man-db.
+Preparing to unpack .../man-db_2.7.3-1_x32.deb ...
+Unpacking man-db (2.7.3-1) ...
+Selecting previously unselected package libffi6:x32.
+Preparing to unpack .../libffi6_3.2.1-3_x32.deb ...
+Unpacking libffi6:x32 (3.2.1-3) ...
+Selecting previously unselected package libunistring0:x32.
+Preparing to unpack .../libunistring0_0.9.3-5.2_x32.deb ...
+Unpacking libunistring0:x32 (0.9.3-5.2) ...
+Selecting previously unselected package libmagic1:x32.
+Preparing to unpack .../libmagic1_1%3a5.25-1_x32.deb ...
+Unpacking libmagic1:x32 (1:5.25-1) ...
+Selecting previously unselected package file.
+Preparing to unpack .../file_1%3a5.25-1_x32.deb ...
+Unpacking file (1:5.25-1) ...
+Selecting previously unselected package gettext-base.
+Preparing to unpack .../gettext-base_0.19.6-1_x32.deb ...
+Unpacking gettext-base (0.19.6-1) ...
+Selecting previously unselected package libicu55:x32.
+Preparing to unpack .../libicu55_55.1-5_x32.deb ...
+Unpacking libicu55:x32 (55.1-5) ...
+Selecting previously unselected package libxml2:x32.
+Preparing to unpack .../libxml2_2.9.2+zdfsg1-4_x32.deb ...
+Unpacking libxml2:x32 (2.9.2+zdfsg1-4) ...
+Selecting previously unselected package libglib2.0-0:x32.
+Preparing to unpack .../libglib2.0-0_2.44.1-1.1_x32.deb ...
+Unpacking libglib2.0-0:x32 (2.44.1-1.1) ...
+Selecting previously unselected package libcroco3:x32.
+Preparing to unpack .../libcroco3_0.6.8-3+b1_x32.deb ...
+Unpacking libcroco3:x32 (0.6.8-3+b1) ...
+Selecting previously unselected package gettext.
+Preparing to unpack .../gettext_0.19.6-1_x32.deb ...
+Unpacking gettext (0.19.6-1) ...
+Selecting previously unselected package intltool-debian.
+Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
+Unpacking intltool-debian (0.35.0+20060710.4) ...
+Selecting previously unselected package po-debconf.
+Preparing to unpack .../po-debconf_1.0.18_all.deb ...
+Unpacking po-debconf (1.0.18) ...
+Selecting previously unselected package debhelper.
+Preparing to unpack .../debhelper_9.20150811_all.deb ...
+Unpacking debhelper (9.20150811) ...
+Selecting previously unselected package libhts1:x32.
+Preparing to unpack .../libhts1_1.2.1-1_x32.deb ...
+Unpacking libhts1:x32 (1.2.1-1) ...
+Selecting previously unselected package libhts-dev:x32.
+Preparing to unpack .../libhts-dev_1.2.1-1_x32.deb ...
+Unpacking libhts-dev:x32 (1.2.1-1) ...
+Selecting previously unselected package libio-pty-perl.
+Preparing to unpack .../libio-pty-perl_1%3a1.08-1+b2_x32.deb ...
+Unpacking libio-pty-perl (1:1.08-1+b2) ...
+Selecting previously unselected package libtinfo-dev:x32.
+Preparing to unpack .../libtinfo-dev_6.0+20150810-1_x32.deb ...
+Unpacking libtinfo-dev:x32 (6.0+20150810-1) ...
+Selecting previously unselected package libncurses5-dev:x32.
+Preparing to unpack .../libncurses5-dev_6.0+20150810-1_x32.deb ...
+Unpacking libncurses5-dev:x32 (6.0+20150810-1) ...
+Selecting previously unselected package tabix.
+Preparing to unpack .../archives/tabix_1.2.1-1_x32.deb ...
+Unpacking tabix (1.2.1-1) ...
+Selecting previously unselected package zlib1g-dev:x32.
+Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_x32.deb ...
+Unpacking zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Selecting previously unselected package sbuild-build-depends-samtools-dummy.
+Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
+Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Setting up bash-completion (1:2.1-4.2) ...
+Setting up groff-base (1.22.3-1) ...
+Setting up bsdmainutils (9.0.6) ...
+update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
+update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
+Setting up libpipeline1:x32 (1.4.1-1) ...
+Setting up man-db (2.7.3-1) ...
+Not building database; man-db/auto-update is not 'true'.
+Setting up libffi6:x32 (3.2.1-3) ...
+Setting up libunistring0:x32 (0.9.3-5.2) ...
+Setting up libmagic1:x32 (1:5.25-1) ...
+Setting up file (1:5.25-1) ...
+Setting up gettext-base (0.19.6-1) ...
+Setting up libicu55:x32 (55.1-5) ...
+Setting up libxml2:x32 (2.9.2+zdfsg1-4) ...
+Setting up libglib2.0-0:x32 (2.44.1-1.1) ...
+No schema files found: doing nothing.
+Setting up libcroco3:x32 (0.6.8-3+b1) ...
+Setting up gettext (0.19.6-1) ...
+Setting up intltool-debian (0.35.0+20060710.4) ...
+Setting up po-debconf (1.0.18) ...
+Setting up debhelper (9.20150811) ...
+Setting up libhts1:x32 (1.2.1-1) ...
+Setting up libhts-dev:x32 (1.2.1-1) ...
+Setting up libio-pty-perl (1:1.08-1+b2) ...
+Setting up libtinfo-dev:x32 (6.0+20150810-1) ...
+Setting up libncurses5-dev:x32 (6.0+20150810-1) ...
+Setting up tabix (1.2.1-1) ...
+Setting up zlib1g-dev:x32 (1:1.2.8.dfsg-2+b1) ...
+Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
+Processing triggers for libc-bin (2.19-20) ...
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build environment │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Kernel: Linux 3.16.0-4-amd64 amd64 (x86_64)
+Toolchain package versions: binutils_2.25.1-1 dpkg-dev_1.18.2 g++-4.9_4.9.3-4 g++-5_5.2.1-17 gcc-4.9_4.9.3-4 gcc-5_5.2.1-17 libc6-dev_2.19-20 libstdc++-4.9-dev_4.9.3-4 libstdc++-5-dev_5.2.1-17 libstdc++6_5.2.1-17 linux-libc-dev_4.1.6-1
+Package versions: adduser_3.113+nmu3 apt_1.0.10.2 base-files_9.4 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.1-1 bsdmainutils_9.0.6 bsdutils_1:2.27-1 build-essential_12.1 bzip2_1.0.6-8 coreutils_8.23-4 cpp_4:5.2.1-4 cpp-4.9_4.9.3-4 cpp-5_5.2.1-17 dash_0.5.7-4 debconf_1.5.57 debconf-i18n_1.5.57 debhelper_9.20150811 debian-archive-keyring_2014.3 debianutils_4.5.1 diffutils_1:3.3-1 dmsetup_2:1.02.104-1 dpkg_1.18.2 dpkg-dev_1.18.2 e2fslibs_1.42.13-1 e2fsprogs_1.42. [...]
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+Unpack source
+─────────────
+
+gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
+gpgv: Signature made Tue Sep 22 14:09:27 2015 UTC using RSA key ID D1C646D1
+gpgv: Can't check signature: public key not found
+dpkg-source: warning: failed to verify signature on ./samtools_1.2-3.dsc
+dpkg-source: info: extracting samtools in samtools-1.2
+dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
+dpkg-source: info: unpacking samtools_1.2-3.debian.tar.xz
+dpkg-source: info: applying fix_segfault_with_small_ref.patch
+dpkg-source: info: applying dynamic-build.patch
+dpkg-source: info: applying i386-build.patch
+
+Check disc space
+────────────────
+
+Sufficient free space for build
+
+User Environment
+────────────────
+
+DEB_BUILD_OPTIONS=nobench nocheck
+HOME=/sbuild-nonexistent
+LD_LIBRARY_PATH=/usr/lib/libeatmydata
+LD_PRELOAD=libeatmydata.so
+LOGNAME=buildd
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
+PWD=/«PKGBUILDDIR»
+SCHROOT_ALIAS_NAME=sid-x32-sbuild
+SCHROOT_CHROOT_NAME=sid-x32-sbuild
+SCHROOT_COMMAND=env
+SCHROOT_GID=122
+SCHROOT_GROUP=buildd
+SCHROOT_SESSION_ID=sid-x32-sbuild-c7419e9a-0e33-4085-9861-ae9bf72219b7
+SCHROOT_UID=114
+SCHROOT_USER=buildd
+SHELL=/bin/sh
+USER=buildd
+XDG_SESSION_ID=c20511
+
+dpkg-buildpackage
+─────────────────
+
+dpkg-buildpackage: source package samtools
+dpkg-buildpackage: source version 1.2-3
+dpkg-buildpackage: source distribution unstable
+ dpkg-source --before-build samtools-1.2
+dpkg-buildpackage: host architecture x32
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+ fakeroot debian/rules clean
+dh clean --parallel
+ dh_testdir -O--parallel
+ dh_auto_clean -O--parallel
+ make -j1 distclean
+make[1]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+rm -f TAGS
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_clean -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ rm -f debian/samtools-test.substvars
+ rm -f debian/samtools-test.*.debhelper
+ rm -rf debian/samtools-test/
+ rm -rf debian/.debhelper/
+ rm -f debian/*.debhelper.log
+ rm -f debian/files
+ find . \( \( \
+ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
+ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
+ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
+ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
+ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
+ \) -exec rm -f {} + \) -o \
+ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
+ rm -f *-stamp
+ debian/rules build-arch
+dh build-arch --parallel
+ dh_testdir -a -O--parallel
+ dh_auto_configure -a -O--parallel
+ debian/rules override_dh_auto_build
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_build -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a \
+ CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
+ CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
+ LDFLAGS="$(dpkg-buildflags --get LDFLAGS)" \
+ LDLIBS="-lhts"
+ make -j1 HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro LDLIBS=-lhts
+make[2]: Entering directory '/«PKGBUILDDIR»'
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
+echo '#define SAMTOOLS_VERSION "1.2"' > version.h
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
+ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
+ar: `u' modifier ignored since `D' is the default (see `U')
+gcc -pthread -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o libbam.a /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lcurses -lm -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
+gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMAQ_LONGREADS -c -o misc/maq2sam-long.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
+gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/md5.o misc/md5.c
+gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o misc/md5.o -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -DMD5SUM_MAIN -c -o misc/md5sum-lite.o misc/md5.c
+gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
+gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lhts -lm -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_pretty_header.o test/merge/test_pretty_header.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_pretty_header test/merge/test_pretty_header.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
+gcc -pthread -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
+gcc -pthread -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
+gcc -pthread -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
+gcc -pthread -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -I. -I/usr/include -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
+gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/x86_64-linux-gnux32/libhts.a -lhts -lz
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ debian/rules override_dh_auto_test
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_test -- \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a \
+ BGZIP=/usr/bin/bgzip
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ fakeroot debian/rules binary-arch
+dh binary-arch --parallel
+ dh_testroot -a -O--parallel
+ dh_prep -a -O--parallel
+ rm -f debian/samtools.substvars
+ rm -f debian/samtools.*.debhelper
+ rm -rf debian/samtools/
+ debian/rules override_dh_auto_install
+make[1]: Entering directory '/«PKGBUILDDIR»'
+dh_auto_install -- \
+ prefix=/usr \
+ HTSDIR="/usr/include" \
+ HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a
+ install -d debian/samtools
+ make -j1 install DESTDIR=/«PKGBUILDDIR»/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr HTSDIR=/usr/include HTSLIB=/usr/lib/x86_64-linux-gnux32/libhts.a
+make[2]: Entering directory '/«PKGBUILDDIR»'
+mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
+install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make clean
+make[2]: Entering directory '/«PKGBUILDDIR»'
+rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
+cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
+rm -f *.o misc/*.o test/*.o test/*/*.o version.h
+rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
+make[2]: Leaving directory '/«PKGBUILDDIR»'
+make[1]: Leaving directory '/«PKGBUILDDIR»'
+ dh_install -a -O--parallel
+ install -d debian/samtools//usr
+ cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
+ install -d debian/samtools//usr/share/man
+ cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
+ dh_installdocs -a -O--parallel
+ install -d debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
+ cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
+ chown -R 0:0 debian/samtools/usr/share/doc
+ chmod -R go=rX debian/samtools/usr/share/doc
+ chmod -R u\+rw debian/samtools/usr/share/doc
+ install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
+ install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
+ dh_installchangelogs -a -O--parallel
+ install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
+ dh_installman -a -O--parallel
+ man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
+ chmod 644 samtools.1.new
+ mv -f samtools.1.new samtools.1
+ dh_perl -a -O--parallel
+ (grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
+ mv debian/samtools.substvars.new debian/samtools.substvars
+ dh_link -a -O--parallel
+ dh_compress -a -O--parallel
+ cd debian/samtools
+ chmod a-x usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ gzip -9nf usr/share/man/man1/samtools.1 usr/share/doc/samtools/changelog.Debian
+ 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 -perm -5 -type f \( -name '*.so.*' -or -name '*.so' -or -name '*.la' -or -name '*.a' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools -perm -5 -type f \( -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
+ find debian/samtools/usr/lib/x86_64-linux-gnux32/perl5/5.20 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
+ find debian/samtools/usr/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
+ dh_strip -a -O--parallel
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
+ strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
+ dh_makeshlibs -a -O--parallel
+ rm -f debian/samtools/DEBIAN/shlibs
+ dh_shlibdeps -a -O--parallel
+ install -d debian/samtools/DEBIAN
+ dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
+dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam were not linked against libhts.so.1 (they use none of the library's symbols)
+ dh_installdeb -a -O--parallel
+ dh_gencontrol -a -O--parallel
+ echo misc:Depends= >> debian/samtools.substvars
+ echo misc:Pre-Depends= >> debian/samtools.substvars
+ dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
+dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
+dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
+ chmod 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
+ dh_builddeb -a -O--parallel
+ dpkg-deb --build debian/samtools ..
+dpkg-deb: building package 'samtools' in '../samtools_1.2-3_x32.deb'.
+ dpkg-genchanges -B -mDebian/x32 buildd <buildd at vs76.physik.fu-berlin.de> >../samtools_1.2-3_x32.changes
+dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
+ dpkg-source --after-build samtools-1.2
+dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
+dpkg-buildpackage: binary-only upload (no source included)
+────────────────────────────────────────────────────────────────────────────────
+Build finished at 20150922-1850
+
+Finished
+────────
+
+I: Built successfully
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build Chroot │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Changes │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_x32.changes:
+───────────────────────────
+
+Format: 1.8
+Date: Tue, 22 Sep 2015 06:42:01 -0700
+Source: samtools
+Binary: samtools samtools-test
+Architecture: x32
+Version: 1.2-3
+Distribution: sid
+Urgency: medium
+Maintainer: Debian/x32 buildd <buildd at vs76.physik.fu-berlin.de>
+Changed-By: Afif Elghraoui <afif at ghraoui.name>
+Description:
+ samtools - processing sequence alignments in SAM and BAM formats
+ samtools-test - test files for the samtools package.
+Closes: 799698
+Changes:
+ samtools (1.2-3) unstable; urgency=medium
+ .
+ * Team upload.
+ [19de55e] Revert "Allow all scripts to be called without language extensions"
+ (Closes: #799698)
+ [658179c] Revert "Remove source files not present in upstream tarball"
+Checksums-Sha1:
+ c9030f2eb987aae2f9ba2f1b7955677e0d07078c 393918 samtools_1.2-3_x32.deb
+Checksums-Sha256:
+ 208e9f733ec483a03337e5ed9b55ecc43e68ee279515cf900fb6e43d344baf3a 393918 samtools_1.2-3_x32.deb
+Files:
+ 5a44c515ed4b9d51d3acf9636d1f15cf 393918 science optional samtools_1.2-3_x32.deb
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Package contents │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+samtools_1.2-3_x32.deb
+──────────────────────
+
+ new debian package, version 2.0.
+ size 393918 bytes: control archive=1486 bytes.
+ 801 bytes, 16 lines control
+ 1557 bytes, 27 lines md5sums
+ Package: samtools
+ Version: 1.2-3
+ Architecture: x32
+ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+ Installed-Size: 1043
+ Depends: libc6 (>= 2.16), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
+ 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
+ to retrieve reads in any regions swiftly. It is designed to work on a stream,
+ and is able to open a BAM (not SAM) file on a remote FTP or HTTP server.
+
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/bin/
+-rwxr-xr-x root/root 17912 2015-09-22 18:50 ./usr/bin/ace2sam
+-rwxr-xr-x root/root 5328 2015-02-02 16:18 ./usr/bin/blast2sam.pl
+-rwxr-xr-x root/root 3364 2015-02-02 16:18 ./usr/bin/bowtie2sam.pl
+-rwxr-xr-x root/root 18032 2015-02-02 16:18 ./usr/bin/export2sam.pl
+-rwxr-xr-x root/root 6125 2015-02-02 16:18 ./usr/bin/interpolate_sam.pl
+-rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-long
+-rwxr-xr-x root/root 9680 2015-09-22 18:50 ./usr/bin/maq2sam-short
+-rwxr-xr-x root/root 13776 2015-09-22 18:50 ./usr/bin/md5fa
+-rwxr-xr-x root/root 9624 2015-09-22 18:50 ./usr/bin/md5sum-lite
+-rwxr-xr-x root/root 6773 2015-02-02 16:18 ./usr/bin/novo2sam.pl
+-rwxr-xr-x root/root 48036 2015-02-02 16:18 ./usr/bin/plot-bamstats
+-rwxr-xr-x root/root 3208 2015-02-02 16:18 ./usr/bin/psl2sam.pl
+-rwxr-xr-x root/root 8961 2015-02-02 16:18 ./usr/bin/sam2vcf.pl
+-rwxr-xr-x root/root 797680 2015-09-22 18:50 ./usr/bin/samtools
+-rwxr-xr-x root/root 16478 2015-02-02 16:18 ./usr/bin/samtools.pl
+-rwxr-xr-x root/root 11105 2015-02-02 16:18 ./usr/bin/seq_cache_populate.pl
+-rwxr-xr-x root/root 3909 2015-02-02 16:18 ./usr/bin/soap2sam.pl
+-rwxr-xr-x root/root 7888 2015-02-02 16:18 ./usr/bin/varfilter.py
+-rwxr-xr-x root/root 18000 2015-09-22 18:50 ./usr/bin/wgsim
+-rwxr-xr-x root/root 4157 2015-02-02 16:18 ./usr/bin/wgsim_eval.pl
+-rwxr-xr-x root/root 3583 2015-02-02 16:18 ./usr/bin/zoom2sam.pl
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/doc/samtools/
+-rw-r--r-- root/root 828 2015-02-02 16:18 ./usr/share/doc/samtools/AUTHORS
+-rw-r--r-- root/root 1031 2015-09-22 16:07 ./usr/share/doc/samtools/README.Debian
+-rw-r--r-- root/root 3629 2015-09-22 16:07 ./usr/share/doc/samtools/changelog.Debian.gz
+-rw-r--r-- root/root 3462 2015-09-22 16:07 ./usr/share/doc/samtools/copyright
+-rw-r--r-- root/root 592 2015-09-22 16:07 ./usr/share/doc/samtools/reference
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/
+drwxr-xr-x root/root 0 2015-09-22 18:50 ./usr/share/man/man1/
+-rw-r--r-- root/root 12907 2015-09-22 18:50 ./usr/share/man/man1/samtools.1.gz
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Post Build │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Cleanup │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Purging /«BUILDDIR»
+Not cleaning session: cloned chroot in use
+
+┌──────────────────────────────────────────────────────────────────────────────┐
+│ Summary │
+└──────────────────────────────────────────────────────────────────────────────┘
+
+Build Architecture: x32
+Build-Space: 14968
+Build-Time: 39
+Distribution: sid
+Host Architecture: x32
+Install-Time: 22
+Job: samtools_1.2-3
+Machine Architecture: amd64
+Package: samtools
+Package-Time: 79
+Source-Version: 1.2-3
+Space: 14968
+Status: successful
+Version: 1.2-3
+────────────────────────────────────────────────────────────────────────────────
+Finished at 20150922-1850
+Build needed 00:01:19, 14968k disc space
+Signature with key 'A644D214' requested:
+ signfile /var/lib/buildd/build/samtools_1.2-3_x32.changes A644D214
+
+Successfully signed changes file
--
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