samtools →
1.2-4 →
armhf → 2015-12-27 06:23:01
sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ samtools 1.2-4 (armhf) 27 Dec 2015 06:09 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: samtools
Version: 1.2-4
Source Version: 1.2-4
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/samtools-9g81ry/samtools-1.2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/samtools-9g81ry' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-ad09207a-e6bc-431a-8041-59f84291f5a6' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8572 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.6 MB]
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│ Fetch source files │
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Check APT
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Building dependency tree...
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NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
git://anonscm.debian.org/debian-med/samtools.git
Please use:
git clone git://anonscm.debian.org/debian-med/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4332 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main samtools 1.2-4 (dsc) [2116 B]
Get:2 http://172.17.0.1/private stretch-staging/main samtools 1.2-4 (tar) [4319 kB]
Get:3 http://172.17.0.1/private stretch-staging/main samtools 1.2-4 (diff) [11.5 kB]
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-ZLhvka/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ Release.gpg [299 B]
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Get:4 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ Sources [188 B]
Get:5 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ Packages [507 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libapt-pkg4.16 libisl13
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 12 not upgraded.
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Get:1 file:/«BUILDDIR»/resolver-ZLhvka/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
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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, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.2), 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, 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-tjYmub/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Get:1 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ InRelease
Ign:1 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ InRelease
Get:2 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Release [2119 B]
Get:2 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Release [2119 B]
Get:3 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Release.gpg [299 B]
Get:3 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Release.gpg [299 B]
Get:4 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Sources [340 B]
Get:5 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ Packages [599 B]
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Install samtools build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libapt-pkg4.16 libisl13
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
bash-completion bsdmainutils debhelper dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1 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 dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libcroco3
libffi6 libfile-stripnondeterminism-perl libglib2.0-0 libhts-dev libhts1
libicu55 libio-pty-perl libmagic1 libncurses5-dev libpipeline1 libtinfo-dev
libunistring0 libxml2 man-db po-debconf sbuild-build-depends-samtools-dummy
tabix zlib1g-dev
0 upgraded, 29 newly installed, 0 to remove and 12 not upgraded.
Need to get 17.6 MB/17.6 MB of archives.
After this operation, 62.3 MB of additional disk space will be used.
Get:1 file:/«BUILDDIR»/resolver-tjYmub/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [864 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-4 [1084 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.6 [177 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-1 [23.9 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf bash-completion all 1:2.1-4.2 [179 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.6-1 [119 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-6 [7379 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-1 [2482 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.6-1 [1393 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.18 [248 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.55-1 [97.4 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.6 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.014-1 [7472 B]
Get:22 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20151225 [830 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.2.1-1+rpi1 [190 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.2.1-1+rpi1 [237 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libio-pty-perl armhf 1:1.08-1.1 [34.9 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20151024-2 [65.8 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20151024-2 [154 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf tabix armhf 1.2.1-1+rpi1 [179 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
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Setting up bsdmainutils (9.0.6) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.25.90.20151209-1 dpkg-dev_1.18.3 g++-5_5.3.1-3+rpi1 gcc-5_5.3.1-3+rpi1 libc6-dev_2.21-4 libstdc++-4.9-dev_4.9.3-5+b1 libstdc++-5-dev_5.3.1-3+rpi1 libstdc++6_5.3.1-3+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-2 adduser_3.113+nmu3 apt_1.1.4 base-files_9.4+rpi1 base-passwd_3.5.38 bash_4.3-14 bash-completion_1:2.1-4.2 binutils_2.25.90.20151209-1 bsdmainutils_9.0.6 bsdutils_1:2.27.1-1 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.23-4 cpio_2.11+dfsg-4.1 cpp_4:5.2.1-4+rpi3 cpp-5_5.3.1-3+rpi1 dash_0.5.7-4 debconf_1.5.58 debfoster_2.7-2 debhelper_9.20151225 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-2 dpkg_1.18.3 dpkg-dev_1.18.3 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.4.2-10 g++_4:5.2.1-4+rpi3 g++-5_5.3.1-3+rpi1 gcc_4:5.2.1-4+rpi3 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-1+b1 gcc-4.9-base_4.9.3-5+b1 gcc-5_5.3.1-3+rpi1 gcc-5-base_5.3.1-3+rpi1 gettext_0.19.6-1 gettext-base_0.19.6-1 gnupg_1.4.19-6 gpgv_1.4.19-6 grep_2.22-1 groff-base_1.22.3-4 gzip_1.6-4 hostname_3.16 init_1.24 init-system-helpers_1.24 initramfs-tools_0.120 initscripts_2.88dsf-59.2 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-4+rpi1 kmod_21-1 libacl1_2.2.52-2 libapparmor1_2.10-2+b2 libapt-pkg4.12_1.0.9.10 libapt-pkg4.16_1.0.10.2 libapt-pkg5.0_1.1.4 libarchive-zip-perl_1.55-1 libasan1_4.9.3-5+b1 libasan2_5.3.1-3+rpi1 libatomic1_5.3.1-3+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4 libaudit1_1:2.4.4-4 libblkid1_2.27.1-1 libbz2-1.0_1.0.6-8 libc-bin_2.21-4 libc-dev-bin_2.21-4 libc6_2.21-4 libc6-dev_2.21-4 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-3+rpi1 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.6.6-5 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1 libdebconfclient0_0.200 libdevmapper1.02.1_2:1.02.110-2 libdpkg-perl_1.18.3 libdrm2_2.4.65-3 libfakeroot_1.20.2-1 libfdisk1_2.27.1-1 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgc1c2_1:7.4.2-7.3 libgcc-4.9-dev_4.9.3-5+b1 libgcc-5-dev_5.3.1-3+rpi1 libgcc1_1:5.3.1-3+rpi1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-1 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-3+rpi1 libgpg-error0_1.20-1 libhts-dev_1.2.1-1+rpi1 libhts1_1.2.1-1+rpi1 libicu55_55.1-6 libio-pty-perl_1:1.08-1.1 libisl13_0.14-2 libisl15_0.15-3 libklibc_2.0.4-4+rpi1 libkmod2_21-1 liblocale-gettext-perl_1.07-1 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-1 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2 libncurses5-dev_6.0+20151024-2 libncursesw5_6.0+20151024-2 libpam-modules_1.1.8-3.1 libpam-modules-bin_1.1.8-3.1 libpam-runtime_1.1.8-3.1 libpam0g_1.1.8-3.1 libpcre3_2:8.35-8 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_2:3.3.9-9 libprocps4_2:3.3.10-2 libreadline6_6.3-8+b3 libseccomp2_2.2.3-2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2+b1 libsmartcols1_2.27.1-1 libss2_1.42.13-1 libstdc++-4.9-dev_4.9.3-5+b1 libstdc++-5-dev_5.3.1-3+rpi1 libstdc++6_5.3.1-3+rpi1 libsystemd0_228-2 libtext-charwidth-perl_0.04-7+b4 libtext-iconv-perl_1.7-5+b5 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20151024-2 libtinfo5_6.0+20151024-2 libubsan0_5.3.1-3+rpi1 libudev1_228-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_4.1+Debian13+rpi1+nmu1 make_4.0-8.2 makedev_2.3.1-93 man-db_2.7.5-1 manpages_3.74-1 mawk_1.3.3-17 mount_2.27.1-1 multiarch-support_2.21-4 nano_2.4.2-1 ncurses-base_6.0+20151024-2 ncurses-bin_6.0+20151024-2 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 po-debconf_1.0.18 procps_2:3.3.10-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_228-2 systemd-sysv_228-2 sysv-rc_2.88dsf-59.2 sysvinit-utils_2.88dsf-59.2 tabix_1.2.1-1+rpi1 tar_1.28-2.1 tzdata_2015g-1 udev_228-2 util-linux_2.27.1-1 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Dec 21 12:52:29 2015 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./samtools_1.2-4.dsc
dpkg-source: info: extracting samtools in samtools-1.2
dpkg-source: info: unpacking samtools_1.2.orig.tar.gz
dpkg-source: info: unpacking samtools_1.2-4.debian.tar.xz
dpkg-source: info: applying fix_segfault_with_small_ref.patch
dpkg-source: info: applying dynamic-build.patch
dpkg-source: info: applying i386-build.patch
dpkg-source: info: applying mayhem.patch
Check disc space
────────────────
Sufficient free space for build
User Environment
────────────────
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-ad09207a-e6bc-431a-8041-59f84291f5a6
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package samtools
dpkg-buildpackage: source version 1.2-4
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.2
dpkg-buildpackage: host architecture armhf
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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/libhts.a -lhts -lz
gcc -pthread -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o /usr/lib/arm-linux-gnueabihf/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-gnueabihf/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-gnueabihf/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-gnueabihf/libhts.a \
BGZIP=/usr/bin/bgzip
make -j4 test HTSDIR=/usr/include HTSLIB=/usr/lib/arm-linux-gnueabihf/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/xrSw7wPIO5/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/xrSw7wPIO5/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/xrSw7wPIO5/bgzip.dat.gz
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/«PKGBUILDDIR»/samtools faidx /tmp/xrSw7wPIO5/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_index:
/«PKGBUILDDIR»/samtools index /tmp/xrSw7wPIO5/large_chrom.bam
.. expected failure
test_index:
/«PKGBUILDDIR»/samtools view /tmp/xrSw7wPIO5/large_chrom.bam ref2
.. ok
test_index:
/«PKGBUILDDIR»/samtools view /tmp/xrSw7wPIO5/large_chrom.bam ref2:1-541556283
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -b /tmp/xrSw7wPIO5/mpileup.bam.list -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -b /tmp/xrSw7wPIO5/mpileup.cram.list -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xrSw7wPIO5/mpileup.bam.list -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -uvDV -b /tmp/xrSw7wPIO5/mpileup.cram.list -f /tmp/xrSw7wPIO5/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/xrSw7wPIO5/mpileup.cram.list -f /tmp/xrSw7wPIO5/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/xrSw7wPIO5/mpileup.cram.list -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xrSw7wPIO5/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/«PKGBUILDDIR»/samtools mpileup -B --ff 0x14 -f /tmp/xrSw7wPIO5/mpileup.ref.fa.gz -r17:1050-1060 /tmp/xrSw7wPIO5/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/xrSw7wPIO5/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/xrSw7wPIO5/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/xrSw7wPIO5/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/xrSw7wPIO5/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/xrSw7wPIO5/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/xrSw7wPIO5/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/xrSw7wPIO5/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/xrSw7wPIO5/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/xrSw7wPIO5/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/xrSw7wPIO5/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/xrSw7wPIO5/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/xrSw7wPIO5/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/xrSw7wPIO5/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/xrSw7wPIO5/view.test067.sam -h -l Library 2 /tmp/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/view.test069.sam -h -l Library 2 /tmp/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/view.test071.sam -h -l Library 2 /tmp/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/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/xrSw7wPIO5/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/bNdbIXzdyx - /«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-gnueabihf/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-gnueabihf/libhts.a
make[2]: Entering directory '/«PKGBUILDDIR»'
mkdir -p -m 755 /«PKGBUILDDIR»/debian/tmp/usr/bin /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /«PKGBUILDDIR»/debian/tmp/usr/bin
install -p -m 644 samtools.1 /«PKGBUILDDIR»/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/«PKGBUILDDIR»'
make clean
make[2]: Entering directory '/«PKGBUILDDIR»'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_pretty_header test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/«PKGBUILDDIR»'
make[1]: Leaving directory '/«PKGBUILDDIR»'
dh_install -a -O--parallel
install -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
chown -R 0:0 debian/samtools/usr/share/doc
chmod -R go=rX debian/samtools/usr/share/doc
chmod -R u\+rw debian/samtools/usr/share/doc
install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
dh_installman -a -O--parallel
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
chmod 644 ace2sam.1.new
mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
chmod 644 samtools.pl.1.new
mv -f samtools.pl.1.new samtools.pl.1
man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
chmod 644 wgsim.1.new
mv -f wgsim.1.new wgsim.1
dh_lintian -a -O--parallel
install -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
cd debian/samtools
chmod a-x usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
gzip -9nf usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/«PKGBUILDDIR»'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/lib/arm-linux-gnueabihf/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 -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/samtools/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/1d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/1d/c554a3331982568d8666bbedc10993dceb15e6.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/1d/c554a3331982568d8666bbedc10993dceb15e6.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/1d/c554a3331982568d8666bbedc10993dceb15e6.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/2e691dd8829b3805730b4a04213cc46a749972.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/2e691dd8829b3805730b4a04213cc46a749972.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/88/2e691dd8829b3805730b4a04213cc46a749972.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9d/8e0195bf6d4b8a621559c9edf09d256003a0a4.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9d/8e0195bf6d4b8a621559c9edf09d256003a0a4.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/9d/8e0195bf6d4b8a621559c9edf09d256003a0a4.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cf
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cf/150d656a70a2530b830e80f1cc19c69d5770b3.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cf/150d656a70a2530b830e80f1cc19c69d5770b3.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/cf/150d656a70a2530b830e80f1cc19c69d5770b3.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7d/2841c8999b20cace2ff18ea68a1e3ba49d4e20.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7d/2841c8999b20cace2ff18ea68a1e3ba49d4e20.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/7d/2841c8999b20cace2ff18ea68a1e3ba49d4e20.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fb
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fb/f4f95ee6c2b91b03d5b8a1486f2c06aee6cced.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fb/f4f95ee6c2b91b03d5b8a1486f2c06aee6cced.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/fb/f4f95ee6c2b91b03d5b8a1486f2c06aee6cced.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/0f1403a4cfb681ff83fa66b2199d1fc6660e16.debug
chmod 0644 debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/0f1403a4cfb681ff83fa66b2199d1fc6660e16.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
objcopy --add-gnu-debuglink debian/.debhelper/samtools/ddeb-root/usr/lib/debug/.build-id/28/0f1403a4cfb681ff83fa66b2199d1fc6660e16.debug debian/samtools/usr/bin/wgsim
install -d debian/.debhelper/samtools/ddeb-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/ddeb-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short were not linked against ld-linux-armhf.so.3 (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/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/samtools 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
install -d debian/.debhelper/samtools/ddeb-root/DEBIAN
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/ddeb-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=1dc554a3331982568d8666bbedc10993dceb15e6 280f1403a4cfb681ff83fa66b2199d1fc6660e16 7d2841c8999b20cace2ff18ea68a1e3ba49d4e20 882e691dd8829b3805730b4a04213cc46a749972 9d8e0195bf6d4b8a621559c9edf09d256003a0a4 cf150d656a70a2530b830e80f1cc19c69d5770b3 fbf4f95ee6c2b91b03d5b8a1486f2c06aee6cced" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
chmod 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
chmod 0644 debian/samtools/DEBIAN/control
chown 0:0 debian/samtools/DEBIAN/control
dh_md5sums -a -O--parallel
(cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/samtools/DEBIAN/md5sums
chown 0:0 debian/samtools/DEBIAN/md5sums
(cd debian/.debhelper/samtools/ddeb-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
chown 0:0 debian/.debhelper/samtools/ddeb-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/ddeb-root ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.2-4_armhf.deb'.
dpkg-deb --build debian/samtools ..
dpkg-deb: building package 'samtools' in '../samtools_1.2-4_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../samtools_1.2-4_armhf.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.2
dpkg-source: info: using options from samtools-1.2/debian/source/options: --single-debian-patch
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20151227-0621
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build Chroot │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
samtools_1.2-4_armhf.changes:
─────────────────────────────
Format: 1.8
Date: Mon, 21 Dec 2015 13:49:05 +0100
Source: samtools
Binary: samtools samtools-test
Architecture: armhf
Version: 1.2-4
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Closes: 716197 716199
Changes:
samtools (1.2-4) unstable; urgency=medium
.
* Team upload
* Fix synopsis
* Fix Vcs-Browser
* Add lintian-override to document that the language extensions are used
internally
* Fix spelling
* Fix Mayhem issues caused by unlimited reads of gz input
Closes: #716199, #716197
* Provide some more manpages
Checksums-Sha1:
7493db2e299172fb0526b9b75105757ec07bd2a1 398916 samtools-dbgsym_1.2-4_armhf.deb
1399d82dd46809132223118c76d822de1c15de71 332692 samtools_1.2-4_armhf.deb
Checksums-Sha256:
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9d7f366a4c7d38e6bed676031814332a33ec4fb46c10e0f3c46197f193542e8d 332692 samtools_1.2-4_armhf.deb
Files:
b744e769b6725984541824f6ad7e1605 398916 debug extra samtools-dbgsym_1.2-4_armhf.deb
f559b3c810f28c6b13e58c4bca1b0471 332692 science optional samtools_1.2-4_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
samtools-dbgsym_1.2-4_armhf.deb
───────────────────────────────
new debian package, version 2.0.
size 398916 bytes: control archive=820 bytes.
646 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.2-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 492
Depends: samtools (= 1.2-4)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
Build-Ids: 1dc554a3331982568d8666bbedc10993dceb15e6 280f1403a4cfb681ff83fa66b2199d1fc6660e16 7d2841c8999b20cace2ff18ea68a1e3ba49d4e20 882e691dd8829b3805730b4a04213cc46a749972 9d8e0195bf6d4b8a621559c9edf09d256003a0a4 cf150d656a70a2530b830e80f1cc19c69d5770b3 fbf4f95ee6c2b91b03d5b8a1486f2c06aee6cced
drwxr-xr-x root/root 0 2015-12-27 06:21 ./
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 400040 2015-12-27 06:20 ./usr/lib/debug/.build-id/1d/c554a3331982568d8666bbedc10993dceb15e6.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/28/
-rw-r--r-- root/root 18584 2015-12-27 06:20 ./usr/lib/debug/.build-id/28/0f1403a4cfb681ff83fa66b2199d1fc6660e16.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/7d/
-rw-r--r-- root/root 13704 2015-12-27 06:20 ./usr/lib/debug/.build-id/7d/2841c8999b20cace2ff18ea68a1e3ba49d4e20.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 18836 2015-12-27 06:20 ./usr/lib/debug/.build-id/88/2e691dd8829b3805730b4a04213cc46a749972.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 11108 2015-12-27 06:20 ./usr/lib/debug/.build-id/9d/8e0195bf6d4b8a621559c9edf09d256003a0a4.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/cf/
-rw-r--r-- root/root 11104 2015-12-27 06:20 ./usr/lib/debug/.build-id/cf/150d656a70a2530b830e80f1cc19c69d5770b3.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/lib/debug/.build-id/fb/
-rw-r--r-- root/root 11040 2015-12-27 06:20 ./usr/lib/debug/.build-id/fb/f4f95ee6c2b91b03d5b8a1486f2c06aee6cced.debug
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2015-12-27 06:20 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.2-4_armhf.deb
────────────────────────
new debian package, version 2.0.
size 332692 bytes: control archive=1607 bytes.
807 bytes, 17 lines control
1828 bytes, 31 lines md5sums
Package: samtools
Version: 1.2-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 945
Depends: libc6 (>= 2.15), libhts1 (>= 1.0), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
Homepage: http://www.htslib.org/
Description: processing sequence alignments in SAM and BAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
one to retrieve reads in any regions swiftly. It is designed to work on a
stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP
server.
drwxr-xr-x root/root 0 2015-12-27 06:20 ./
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/bin/
-rwxr-xr-x root/root 17976 2015-12-27 06:20 ./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 9772 2015-12-27 06:20 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9772 2015-12-27 06:20 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 13864 2015-12-27 06:20 ./usr/bin/md5fa
-rwxr-xr-x root/root 9740 2015-12-27 06:20 ./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 690568 2015-12-27 06:20 ./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 18036 2015-12-27 06:20 ./usr/bin/wgsim
-rwxr-xr-x root/root 4157 2015-02-02 15:18 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2015-02-02 15:18 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/doc/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2015-02-02 15:18 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 1031 2015-12-21 12:50 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 3792 2015-12-21 12:50 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 3462 2015-12-21 12:50 ./usr/share/doc/samtools/copyright
-rw-r--r-- root/root 592 2015-12-21 12:50 ./usr/share/doc/samtools/reference
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/lintian/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 219 2015-12-21 12:50 ./usr/share/lintian/overrides/samtools
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/man/
drwxr-xr-x root/root 0 2015-12-27 06:20 ./usr/share/man/man1/
-rw-r--r-- root/root 462 2015-12-27 06:20 ./usr/share/man/man1/ace2sam.1.gz
-rw-r--r-- root/root 12907 2015-12-27 06:20 ./usr/share/man/man1/samtools.1.gz
-rw-r--r-- root/root 410 2015-12-27 06:20 ./usr/share/man/man1/samtools.pl.1.gz
-rw-r--r-- root/root 518 2015-12-27 06:20 ./usr/share/man/man1/wgsim.1.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 15664
Build-Time: 491
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 191
Job: samtools_1.2-4
Machine Architecture: armhf
Package: samtools
Package-Time: 728
Source-Version: 1.2-4
Space: 15664
Status: successful
Version: 1.2-4
────────────────────────────────────────────────────────────────────────────────
Finished at 20151227-0621
Build needed 00:12:08, 15664k disc space