samtools →
1.3.1-1 →
armhf → 2016-05-03 14:53:48
sbuild (Debian sbuild) 0.66.0 (04 Oct 2015) on bm-wb-02
+==============================================================================+
| samtools 1.3.1-1 (armhf) 03 May 2016 14:37 |
+==============================================================================+
Package: samtools
Version: 1.3.1-1
Source Version: 1.3.1-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/samtools-CcdhTH/samtools-1.3.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-CcdhTH' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-30ea4279-7d28-4d60-9423-d89afaf94488' 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 [8942 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.0 MB]
Fetched 20.0 MB in 21s (911 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'samtools' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/samtools.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/samtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3771 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main samtools 1.3.1-1 (dsc) [2164 B]
Get:2 http://172.17.0.1/private stretch-staging/main samtools 1.3.1-1 (tar) [3757 kB]
Get:3 http://172.17.0.1/private stretch-staging/main samtools 1.3.1-1 (diff) [11.9 kB]
Fetched 3771 kB in 0s (9775 kB/s)
Download complete and in download only mode
Check architectures
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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-bfnWYZ/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Sources [194 B]
Get:5 file:/<<BUILDDIR>>/resolver-bfnWYZ/apt_archive ./ Packages [507 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-bfnWYZ/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install core build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 0 B/764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-bfnWYZ/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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W: No sandbox user '_apt' on the system, can not drop privileges
Merged Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
Filtered Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.3), zlib1g-dev, automake, autoconf-archive, tabix (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-oYTEgM/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Sources [258 B]
Get:5 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ Packages [576 B]
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: file:///<<BUILDDIR>>/resolver-oYTEgM/apt_archive/./Release.gpg: Signature by key 3493EC2B8E6DC280C121C60435506D9A48F77B2E uses weak digest algorithm (SHA1)
Reading package lists...
+------------------------------------------------------------------------------+
| Install samtools build dependencies (apt-based resolver) |
+------------------------------------------------------------------------------+
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
libtinfo-dev libtool libunistring0 libxml2 m4 man-db po-debconf tabix
zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff gnutls-bin krb5-doc
krb5-user ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur ca-certificates libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libsasl2-modules libltdl-dev xml-core
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf autoconf-archive automake autopoint autotools-dev bash-completion
bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism file gettext
gettext-base groff-base intltool-debian libarchive-zip-perl libbsd0
libcroco3 libcurl3-gnutls libffi6 libfile-stripnondeterminism-perl
libglib2.0-0 libgnutls30 libgssapi-krb5-2 libhogweed4 libhts-dev libhts1
libicu55 libidn11 libio-pty-perl libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libldap-2.4-2 libmagic1 libncurses5-dev libnettle6
libnghttp2-14 libp11-kit0 libpipeline1 librtmp1 libsasl2-2
libsasl2-modules-db libsigsegv2 libssh2-1 libssl1.0.2 libtasn1-6
libtinfo-dev libtool libunistring0 libxml2 m4 man-db po-debconf
sbuild-build-depends-samtools-dummy tabix zlib1g-dev
0 upgraded, 58 newly installed, 0 to remove and 42 not upgraded.
Need to get 24.1 MB/24.1 MB of archives.
After this operation, 83.8 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-oYTEgM/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [834 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.10 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf bash-completion all 1:2.1-4.3 [178 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf autoconf-archive all 20150925-1 [688 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-2 [886 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libnettle6 armhf 3.2-1 [202 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libhogweed4 armhf 3.2-1 [126 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libidn11 armhf 1.32-3 [110 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libp11-kit0 armhf 0.23.2-3 [93.3 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libtasn1-6 armhf 4.8-1 [44.1 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libgnutls30 armhf 3.4.11-4 [718 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-8 [11.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.13.2+dfsg-5 [56.6 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.13.2+dfsg-5 [110 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.13.2+dfsg-5 [259 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.13.2+dfsg-5 [130 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libsasl2-modules-db armhf 2.1.26.dfsg1-15 [65.6 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libsasl2-2 armhf 2.1.26.dfsg1-15 [96.7 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libldap-2.4-2 armhf 2.4.42+dfsg-2+rpi1+b2 [198 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.7-2 [424 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.48.0-1 [2540 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.57-1 [95.1 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:45 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-0.1 [200 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160403 [800 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.9.2-1 [65.7 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d-1+b1 [54.4 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.5.0-2.1 [121 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libcurl3-gnutls armhf 7.47.0-1 [244 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libhts1 armhf 1.3.1-1+rpi1 [215 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libhts-dev armhf 1.3.1-1+rpi1 [270 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf libio-pty-perl armhf 1:1.08-1.1+b1 [33.0 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160319-1 [65.7 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160319-1 [153 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf tabix armhf 1.3.1-1+rpi1 [203 kB]
Get:58 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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Unpacking automake (1:1.15-4) ...
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Unpacking autopoint (0.19.7-2) ...
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Unpacking libglib2.0-0:armhf (2.48.0-1) ...
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Unpacking libcroco3:armhf (0.6.11-1) ...
Selecting previously unselected package gettext.
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Unpacking gettext (0.19.7-2) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.4) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../po-debconf_1.0.19_all.deb ...
Unpacking po-debconf (1.0.19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../libarchive-zip-perl_1.57-1_all.deb ...
Unpacking libarchive-zip-perl (1.57-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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Unpacking libfile-stripnondeterminism-perl (0.016-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../dh-strip-nondeterminism_0.016-1_all.deb ...
Unpacking dh-strip-nondeterminism (0.016-1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../libtool_2.4.6-0.1_all.deb ...
Unpacking libtool (2.4.6-0.1) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../dh-autoreconf_12_all.deb ...
Unpacking dh-autoreconf (12) ...
Selecting previously unselected package debhelper.
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Unpacking debhelper (9.20160403) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../libnghttp2-14_1.9.2-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.9.2-1) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d-1+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../libssh2-1_1.5.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.5.0-2.1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../libcurl3-gnutls_7.47.0-1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.47.0-1) ...
Selecting previously unselected package libhts1:armhf.
Preparing to unpack .../libhts1_1.3.1-1+rpi1_armhf.deb ...
Unpacking libhts1:armhf (1.3.1-1+rpi1) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../libhts-dev_1.3.1-1+rpi1_armhf.deb ...
Unpacking libhts-dev:armhf (1.3.1-1+rpi1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../libio-pty-perl_1%3a1.08-1.1+b1_armhf.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b1) ...
Selecting previously unselected package libtinfo-dev:armhf.
Preparing to unpack .../libtinfo-dev_6.0+20160319-1_armhf.deb ...
Unpacking libtinfo-dev:armhf (6.0+20160319-1) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../libncurses5-dev_6.0+20160319-1_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.0+20160319-1) ...
Selecting previously unselected package tabix.
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Unpacking tabix (1.3.1-1+rpi1) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package sbuild-build-depends-samtools-dummy.
Preparing to unpack .../sbuild-build-depends-samtools-dummy.deb ...
Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-5) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up bsdmainutils (9.0.10) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up bash-completion (1:2.1-4.3) ...
Setting up autoconf-archive (20150925-1) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libssl1.0.2:armhf (1.0.2g-2) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libnettle6:armhf (3.2-1) ...
Setting up libhogweed4:armhf (3.2-1) ...
Setting up libidn11:armhf (1.32-3) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libp11-kit0:armhf (0.23.2-3) ...
Setting up libtasn1-6:armhf (4.8-1) ...
Setting up libgnutls30:armhf (3.4.11-4) ...
Setting up libkeyutils1:armhf (1.5.9-8) ...
Setting up libkrb5support0:armhf (1.13.2+dfsg-5) ...
Setting up libk5crypto3:armhf (1.13.2+dfsg-5) ...
Setting up libkrb5-3:armhf (1.13.2+dfsg-5) ...
Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-5) ...
Setting up libsasl2-modules-db:armhf (2.1.26.dfsg1-15) ...
Setting up libsasl2-2:armhf (2.1.26.dfsg1-15) ...
Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2+rpi1+b2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up m4 (1.4.17-5) ...
Setting up autoconf (2.69-10) ...
Setting up autotools-dev (20150820.1) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up autopoint (0.19.7-2) ...
Setting up libglib2.0-0:armhf (2.48.0-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.57-1) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtool (2.4.6-0.1) ...
Setting up libnghttp2-14:armhf (1.9.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d-1+b1) ...
Setting up libssh2-1:armhf (1.5.0-2.1) ...
Setting up libcurl3-gnutls:armhf (7.47.0-1) ...
Setting up libhts1:armhf (1.3.1-1+rpi1) ...
Setting up libhts-dev:armhf (1.3.1-1+rpi1) ...
Setting up libio-pty-perl (1:1.08-1.1+b1) ...
Setting up libtinfo-dev:armhf (6.0+20160319-1) ...
Setting up libncurses5-dev:armhf (6.0+20160319-1) ...
Setting up tabix (1.3.1-1+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (9.20160403) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Processing triggers for libc-bin (2.22-5) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-8 dpkg-dev_1.18.4 g++-5_5.3.1-14 gcc-5_5.3.1-14 libc6-dev_2.22-5 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.114 apt_1.2.10 autoconf_2.69-10 autoconf-archive_20150925-1 automake_1:1.15-4 autopoint_0.19.7-2 autotools-dev_20150820.1 base-files_9.6+rpi1 base-passwd_3.5.39 bash_4.3-14 bash-completion_1:2.1-4.3 binutils_2.26-8 bsdmainutils_9.0.10 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-14 dash_0.5.8-2.2 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160403 debianutils_4.7 dh-autoreconf_12 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.120-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.43~WIP.2016.03.15-2 e2fsprogs_1.43~WIP.2016.03.15-2 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-14 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-14 gcc-5-base_5.3.1-14 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-5 gpgv_1.4.20-5 grep_2.22-1 groff-base_1.22.3-7 gzip_1.6-5 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10-4 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.2.10 libarchive-zip-perl_1.57-1 libasan1_4.9.3-12 libasan2_5.3.1-14 libatomic1_5.3.1-14 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-5 libc-dev-bin_2.22-5 libc6_2.22-5 libc6-dev_2.22-5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-14 libcomerr2_1.43~WIP.2016.03.15-2 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libcurl3-gnutls_7.47.0-1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.208 libdevmapper1.02.1_2:1.02.120-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.4 libgcc-4.9-dev_4.9.3-12 libgcc-5-dev_5.3.1-14 libgcc1_1:5.3.1-14 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.48.0-1 libgmp10_2:6.1.0+dfsg-2 libgnutls30_3.4.11-4 libgomp1_5.3.1-14 libgpg-error0_1.21-2 libgssapi-krb5-2_1.13.2+dfsg-5 libhogweed4_3.2-1 libhts-dev_1.3.1-1+rpi1 libhts1_1.3.1-1+rpi1 libicu55_55.1-7 libidn11_1.32-3 libio-pty-perl_1:1.08-1.1+b1 libisl15_0.16.1-1 libk5crypto3_1.13.2+dfsg-5 libkeyutils1_1.5.9-8 libklibc_2.0.4-8+rpi1 libkmod2_22-1.1 libkrb5-3_1.13.2+dfsg-5 libkrb5support0_1.13.2+dfsg-5 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b2 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160319-1 libncurses5-dev_6.0+20160319-1 libncursesw5_6.0+20160319-1 libnettle6_3.2-1 libnghttp2-14_1.9.2-1 libp11-kit0_0.23.2-3 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3.1 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps5_2:3.3.11-3 libreadline6_6.3-8+b3 librtmp1_2.4+20151223.gitfa8646d-1+b1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.0-1 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsigsegv2_2.10-5 libslang2_2.3.0-2.3 libsmartcols1_2.27.1-6 libss2_1.43~WIP.2016.03.15-2 libssh2-1_1.5.0-2.1 libssl1.0.2_1.0.2g-2 libstdc++-4.9-dev_4.9.3-12 libstdc++-5-dev_5.3.1-14 libstdc++6_5.3.1-14 libsystemd0_229-4 libtasn1-6_4.8-1 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160319-1 libtinfo5_6.0+20160319-1 libtool_2.4.6-0.1 libubsan0_5.3.1-14 libudev1_229-4 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libxml2_2.9.3+dfsg1-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.05-1 mawk_1.3.3-17 mount_2.27.1-6 multiarch-support_2.22-5 nano_2.5.3-2 ncurses-base_6.0+20160319-1 ncurses-bin_6.0+20160319-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 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_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-4 systemd-sysv_229-4 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tabix_1.3.1-1+rpi1 tar_1.28-2.1 tzdata_2016c-0+deb8u1 udev_229-4 util-linux_2.27.1-6 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 Tue Apr 26 12:12:42 2016 UTC using RSA key ID 2295D502
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./samtools_1.3.1-1.dsc
dpkg-source: info: extracting samtools in samtools-1.3.1
dpkg-source: info: unpacking samtools_1.3.1.orig.tar.gz
dpkg-source: info: unpacking samtools_1.3.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-30ea4279-7d28-4d60-9423-d89afaf94488
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package samtools
dpkg-buildpackage: source version 1.3.1-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build samtools-1.3.1
dpkg-buildpackage: host architecture armhf
dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
fakeroot debian/rules clean
dh clean --parallel
dh_testdir -O--parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
touch config.mk
dh_auto_clean --
make -j4 distclean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
rm -f config.cache config.h config.log config.mk config.status
rm -f TAGS
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean -O--parallel
rm -f debian/debhelper-build-stamp
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
rm -f debian/samtools-test.substvars
rm -f debian/samtools-test.*.debhelper
rm -rf debian/samtools-test/
rm -rf debian/.debhelper/
rm -f debian/*.debhelper.log
rm -f debian/files
find . \( \( \
\( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS \) -prune -o -type f -a \
\( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \
-o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \
-o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \
-o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \
\) -exec rm -f {} + \) -o \
\( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \)
rm -f *-stamp
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
touch config.mk
aclocal --force -I /usr/share/aclocal/ -I debian/
configure.ac:42: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
configure.ac:42: the top level
autoconf
configure.ac:42: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
debian/ax_with_htslib.m4:53: AX_WITH_HTSLIB is expanded from...
configure.ac:42: the top level
dh_auto_configure -- --with-htslib=system
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking --with-htslib=system
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking for NcursesW wide-character library... no
checking for Ncurses library... yes
checking for working ncurses/curses.h... no
checking for working ncurses.h... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- \
CFLAGS="$(dpkg-buildflags --get CFLAGS)" \
CPPFLAGS="\$(DFLAGS) \$(INCLUDES) $(dpkg-buildflags --get CPPFLAGS)" \
LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"
make -j4 "CFLAGS=-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "CPPFLAGS=\$(DFLAGS) \$(INCLUDES) -Wdate-time -D_FORTIFY_SOURCE=2" LDFLAGS=-Wl,-z,relro
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_index.o bam_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plcmd.o bam_plcmd.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_view.o sam_view.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_cat.o bam_cat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_md.o bam_md.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_reheader.o bam_reheader.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_sort.o bam_sort.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o kprobaln.o kprobaln.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdup.o bam_rmdup.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_rmdupse.o bam_rmdupse.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_mate.o bam_mate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_stat.o bam_stat.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_color.o bam_color.c
echo '#define SAMTOOLS_VERSION "1.3.1"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf_indel.o bam2bcf_indel.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o errmod.o errmod.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_opts.o sam_opts.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o cut_target.o cut_target.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats_isize.o stats_isize.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_flags.o bam_flags.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_split.o bam_split.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview.o bam_tview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_curses.o bam_tview_curses.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_tview_html.o bam_tview_html.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_lpileup.o bam_lpileup.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_quickcheck.o bam_quickcheck.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_addrprg.o bam_addrprg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_aux.o bam_aux.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_import.o bam_import.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_header.o sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam_plbuf.o bam_plbuf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/ace2sam.o misc/ace2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DMAQ_LONGREADS -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-long.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/maq2sam-short.o misc/maq2sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5fa.o misc/md5fa.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/md5sum-lite.o misc/md5sum-lite.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o misc/wgsim.o misc/wgsim.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_bam_translate.o test/merge/test_bam_translate.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/test.o test/test.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_rtrans_build.o test/merge/test_rtrans_build.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/merge/test_trans_tbl_init.o test/merge/test_trans_tbl_init.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_count_rg.o test/split/test_count_rg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_expand_format_string.o test/split/test_expand_format_string.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_filter_header_rg.o test/split/test_filter_header_rg.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/split/test_parse_args.o test/split/test_parse_args.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o test/vcf-miniview.o test/vcf-miniview.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamtk.o bamtk.c
ar -csru libbam.a bam_aux.o bam.o bam_import.o sam.o sam_header.o bam_plbuf.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz -ldl
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz -ldl
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz -ldl
gcc -rdynamic -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz -ldl
gcc -rdynamic -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz -ldl
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o samtools bam_index.o bam_plcmd.o sam_view.o bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o bam_quickcheck.o bam_addrprg.o libbam.a -lhts -lncurses -lm -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o sam_opts.o -lhts -lz -ldl
gcc -pthread -rdynamic -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o sam_opts.o -lhts -lz -ldl
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_test -- \
BGZIP=/usr/bin/bgzip
make -j4 test VERBOSE=1 BGZIP=/usr/bin/bgzip
make[2]: Entering directory '/<<PKGBUILDDIR>>'
REF_PATH=: test/test.pl --exec bgzip=/usr/bin/bgzip
/usr/bin/bgzip -c -b 65272 -s 5 /tmp/3LEoPPqrtz/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/3LEoPPqrtz/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/3LEoPPqrtz/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3LEoPPqrtz/faidx.fa.gz 1:99998-100007 | grep -v '^>'
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /<<PKGBUILDDIR>>/test/dat/dict.fa
.. ok
test_dict:
/<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz /tmp/3LEoPPqrtz/dict.fa.gz
.. ok
test_dict:
cat /<<PKGBUILDDIR>>/test/dat/dict.fa | /<<PKGBUILDDIR>>/samtools dict -a hf37d5 -s 'Homo floresiensis' -u ftp://orthanc.org/hf37d5.fa.gz
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /tmp/3LEoPPqrtz/large_chrom.bam
ERR:
.. expected failure
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/3LEoPPqrtz/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/3LEoPPqrtz/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam && cat /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam.bai
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/3LEoPPqrtz/mpileup.bam.list -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/3LEoPPqrtz/mpileup.cram.list -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/3LEoPPqrtz/mpileup.bam.list -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/3LEoPPqrtz/mpileup.cram.list -f /tmp/3LEoPPqrtz/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/3LEoPPqrtz/mpileup.cram.list -f /tmp/3LEoPPqrtz/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/3LEoPPqrtz/mpileup.cram.list -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/3LEoPPqrtz/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/3LEoPPqrtz/mpileup.ref.fa.gz -r17:1050-1060 /tmp/3LEoPPqrtz/mpileup.1.cram | grep -v mpileup
.. ok
test_usage:
samtools
samtools has subcommands: dict, faidx, index, calmd, fixmate, reheader, rmdup, targetcut, addreplacerg, collate, cat, merge, mpileup, sort, split, quickcheck, fastq, fasta, bedcov, depth, flagstat, idxstats, phase, stats, flags, tview, view, depad
.. ok
test_usage_subcommand:
samtools dict
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools faidx
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools index
.. ok
test_usage_subcommand:
samtools calmd
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools fixmate
.. ok
test_usage_subcommand:
samtools reheader
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools rmdup
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools targetcut
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools addreplacerg
.. ok
test_usage_subcommand:
samtools collate
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools cat
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools merge
.. ok
test_usage_subcommand:
samtools mpileup
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools sort
.. ok
test_usage_subcommand:
samtools split
.. ok
test_usage_subcommand:
samtools quickcheck
.. ok
test_usage_subcommand:
samtools fastq
.. ok
test_usage_subcommand:
samtools fasta
.. ok
test_usage_subcommand:
samtools bedcov
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools depth
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools flagstat
.. ok
test_usage_subcommand:
samtools idxstats
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools phase
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools stats
.. ok
test_usage_subcommand:
samtools flags
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools tview
Usage on stderr rather than stdout
.. expected failure
test_usage_subcommand:
samtools view
.. ok
test_usage_subcommand:
samtools depad
Usage on stderr rather than stdout
.. expected failure
test_view:
Generating test data file .................. done
1: SAM -> BAM -> SAM .. ok
2: SAM -> uncompressed BAM .. ok
3: uncompressed BAM -> SAM and compare .. ok
4: SAM -> fast compressed BAM .. ok
5: fast compressed BAM -> SAM and compare .. ok
6: SAM -> CRAM -> SAM (UR header tags) .. ok
7: SAM -> CRAM -> SAM (M5 header tags) .. ok
8: BAM -> CRAM with UR -> SAM .. ok
9: SAM -> BAM (M5 header tags) .. ok
10: SAM -> BAM -> CRAM -> SAM (M5 header tags) .. ok
11: CRAM -> BAM with UR .. ok
12: CRAM -> BAM with M5 .. ok
13: SAM -> SAM via stdout .. ok
14: SAM -> BAM via stdout .. ok
15: SAM -> CRAM via stdout .. ok
16: SAM from stdin -> SAM .. ok
17: BAM from stdin -> SAM .. ok
18: CRAM from stdin -> SAM .. ok
19: samtools view -H (SAM input) .. ok
20: samtools view -H (BAM input) .. ok
21: samtools view -H (CRAM input) .. ok
22: No headers (SAM input) .. ok
23: No headers (BAM input) .. ok
24: No headers (CRAM input) .. ok
25: Filter -f 128 (SAM input) .. ok
26: Count -f 128 (SAM input) .. ok
27: Filter -f 128 (BAM input) .. ok
28: Count -f 128 (BAM input) .. ok
29: Filter -f 128 (CRAM input) .. ok
30: Count -f 128 (CRAM input) .. ok
31: Filter -F 128 (SAM input) .. ok
32: Count -F 128 (SAM input) .. ok
33: Filter -F 128 (BAM input) .. ok
34: Count -F 128 (BAM input) .. ok
35: Filter -F 128 (CRAM input) .. ok
36: Count -F 128 (CRAM input) .. ok
37: Filter -F 128 -f 2 (SAM input) .. ok
38: Count -F 128 -f 2 (SAM input) .. ok
39: Filter -F 128 -f 2 (BAM input) .. ok
40: Count -F 128 -f 2 (BAM input) .. ok
41: Filter -F 128 -f 2 (CRAM input) .. ok
42: Count -F 128 -f 2 (CRAM input) .. ok
43: Filter -r grp2 (SAM input) .. ok
44: Count -r grp2 (SAM input) .. ok
45: Filter -r grp2 (BAM input) .. ok
46: Count -r grp2 (BAM input) .. ok
47: Filter -r grp2 (CRAM input) .. ok
48: Count -r grp2 (CRAM input) .. ok
49: Filter -R /tmp/3LEoPPqrtz/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/3LEoPPqrtz/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/3LEoPPqrtz/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/3LEoPPqrtz/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/3LEoPPqrtz/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/3LEoPPqrtz/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/3LEoPPqrtz/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/3LEoPPqrtz/view.001.fogn (CRAM input).. ok
67: Filter -l Library 2 (SAM input) .. ok
68: Count -l Library 2 (SAM input) .. ok
69: Filter -l Library 2 (BAM input) .. ok
70: Count -l Library 2 (BAM input) .. ok
71: Filter -l Library 2 (CRAM input) .. ok
72: Count -l Library 2 (CRAM input) .. ok
73: Filter -l Library 3 (SAM input) .. ok
74: Count -l Library 3 (SAM input) .. ok
75: Filter -l Library 3 (BAM input) .. ok
76: Count -l Library 3 (BAM input) .. ok
77: Filter -l Library 3 (CRAM input) .. ok
78: Count -l Library 3 (CRAM input) .. ok
79: Filter -q 50 (SAM input) .. ok
80: Count -q 50 (SAM input) .. ok
81: Filter -q 50 (BAM input) .. ok
82: Count -q 50 (BAM input) .. ok
83: Filter -q 50 (CRAM input) .. ok
84: Count -q 50 (CRAM input) .. ok
85: Filter -q 99 (SAM input) .. ok
86: Count -q 99 (SAM input) .. ok
87: Filter -q 99 (BAM input) .. ok
88: Count -q 99 (BAM input) .. ok
89: Filter -q 99 (CRAM input) .. ok
90: Count -q 99 (CRAM input) .. ok
91: Filter -q 100 (SAM input) .. ok
92: Count -q 100 (SAM input) .. ok
93: Filter -q 100 (BAM input) .. ok
94: Count -q 100 (BAM input) .. ok
95: Filter -q 100 (CRAM input) .. ok
96: Count -q 100 (CRAM input) .. ok
97: Filter -x fa (SAM input) .. ok
98: Count -x fa (SAM input) .. ok
99: Filter -x fa (BAM input) .. ok
100: Count -x fa (BAM input) .. ok
101: Filter -x fa (CRAM input) .. ok
102: Count -x fa (CRAM input) .. ok
103: Filter -x fa -x ha (SAM input) .. ok
104: Count -x fa -x ha (SAM input) .. ok
105: Filter -x fa -x ha (BAM input) .. ok
106: Count -x fa -x ha (BAM input) .. ok
107: Filter -x fa -x ha (CRAM input) .. ok
108: Count -x fa -x ha (CRAM input) .. ok
109: Filter -x fa -r grp2 (SAM input) .. ok
110: Count -x fa -r grp2 (SAM input) .. ok
111: Filter -x fa -r grp2 (BAM input) .. ok
112: Count -x fa -r grp2 (BAM input) .. ok
113: Filter -x fa -r grp2 (CRAM input) .. ok
114: Count -x fa -r grp2 (CRAM input) .. ok
115: Filter -x RG -r grp2 (SAM input) .. ok
116: Count -x RG -r grp2 (SAM input) .. ok
117: Filter -x RG -r grp2 (BAM input) .. ok
118: Count -x RG -r grp2 (BAM input) .. ok
119: Filter -x RG -r grp2 (CRAM input) .. ok
120: Count -x RG -r grp2 (CRAM input) .. ok
121: Filter -m 10 (SAM input) .. ok
122: Count -m 10 (SAM input) .. ok
123: Filter -m 10 (BAM input) .. ok
124: Count -m 10 (BAM input) .. ok
125: Filter -m 10 (CRAM input) .. ok
126: Count -m 10 (CRAM input) .. ok
127: Filter -m 11 (SAM input) .. ok
128: Count -m 11 (SAM input) .. ok
129: Filter -m 11 (BAM input) .. ok
130: Count -m 11 (BAM input) .. ok
131: Filter -m 11 (CRAM input) .. ok
132: Count -m 11 (CRAM input) .. ok
133: Filter -m 15 (SAM input) .. ok
134: Count -m 15 (SAM input) .. ok
135: Filter -m 15 (BAM input) .. ok
136: Count -m 15 (BAM input) .. ok
137: Filter -m 15 (CRAM input) .. ok
138: Count -m 15 (CRAM input) .. ok
139: Filter -m 16 (SAM input) .. ok
140: Count -m 16 (SAM input) .. ok
141: Filter -m 16 (BAM input) .. ok
142: Count -m 16 (BAM input) .. ok
143: Filter -m 16 (CRAM input) .. ok
144: Count -m 16 (CRAM input) .. ok
145: 1bp reads file SAM -> BAM -> SAM .. ok
146: 1bp reads file SAM -> CRAM -> SAM .. ok
146: Region Z (BAM input) .. ok
147: Count Z (BAM input) .. ok
148: Region Z (CRAM input) .. ok
149: Count Z (CRAM input) .. ok
150: Region Z:30 (BAM input) .. ok
151: Count Z:30 (BAM input) .. ok
152: Region Z:30 (CRAM input) .. ok
153: Count Z:30 (CRAM input) .. ok
154: Region Z:20-40 (BAM input) .. ok
155: Count Z:20-40 (BAM input) .. ok
156: Region Z:20-40 (CRAM input) .. ok
157: Count Z:20-40 (CRAM input) .. ok
158: Region ref1 (BAM input) .. ok
159: Count ref1 (BAM input) .. ok
160: Region ref1 (CRAM input) .. ok
161: Count ref1 (CRAM input) .. ok
162: Region ref1:15 (BAM input) .. ok
163: Count ref1:15 (BAM input) .. ok
164: Region ref1:15 (CRAM input) .. ok
165: Count ref1:15 (CRAM input) .. ok
166: Region ref1:15-45 (BAM input) .. ok
167: Count ref1:15-45 (BAM input) .. ok
168: Region ref1:15-45 (CRAM input) .. ok
169: Count ref1:15-45 (CRAM input) .. ok
170: Region ref1:15-45 ref2 (BAM input) .. ok
171: Count ref1:15-45 ref2 (BAM input) .. ok
172: Region ref1:15-45 ref2 (CRAM input) .. ok
173: Count ref1:15-45 ref2 (CRAM input) .. ok
174: Region ref1:15-45 ref2:16 (BAM input) .. ok
175: Count ref1:15-45 ref2:16 (BAM input) .. ok
176: Region ref1:15-45 ref2:16 (CRAM input) .. ok
177: Count ref1:15-45 ref2:16 (CRAM input) .. ok
178: Region ref1:15-45 ref2:16-31 (BAM input) .. ok
179: Count ref1:15-45 ref2:16-31 (BAM input) .. ok
180: Region ref1:15-45 ref2:16-31 (CRAM input) .. ok
181: Count ref1:15-45 ref2:16-31 (CRAM input) .. ok
182: Region ref1:15-15 ref1:45-45 (BAM input) .. ok
183: Count ref1:15-15 ref1:45-45 (BAM input) .. ok
184: Region ref1:15-15 ref1:45-45 (CRAM input) .. ok
185: Count ref1:15-15 ref1:45-45 (CRAM input) .. ok
186: Region -f 128 ref1 (BAM input) .. ok
187: Count -f 128 ref1 (BAM input) .. ok
188: Region -f 128 ref1 (CRAM input) .. ok
189: Count -f 128 ref1 (CRAM input) .. ok
190: Region -q 50 ref1:15-45 (BAM input) .. ok
191: Count -q 50 ref1:15-45 (BAM input) .. ok
192: Region -q 50 ref1:15-45 (CRAM input) .. ok
193: Count -q 50 ref1:15-45 (CRAM input) .. ok
194: Region -r grp2 ref1:15-45 (BAM input) .. ok
195: Count -r grp2 ref1:15-45 (BAM input) .. ok
196: Region -r grp2 ref1:15-45 (CRAM input) .. ok
197: Count -r grp2 ref1:15-45 (CRAM input) .. ok
198: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
199: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
200: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
201: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
202: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
203: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
204: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
205: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
206: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
207: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
208: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
209: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
210: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
211: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
212: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
213: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
214: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
215: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
216: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
217: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
218: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
219: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
220: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
221: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
222: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
223: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
224: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
225: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
226: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
227: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
228: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
229: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
230: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
231: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
232: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
233: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
234: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
235: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
236: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
237: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
238: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
239: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
240: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
241: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
242: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
243: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
244: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
245: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
246: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
247: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
248: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
249: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
250: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
251: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
252: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
253: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
254: Make BAM with no M5/UR tags .. ok
255: Add @SQ with -t (SAM -> SAM) .. ok
256: Add @SQ with -T (SAM -> SAM) .. ok
257: Add @SQ with -t (BAM -> SAM) .. ok
258: Add @SQ with -T (BAM -> SAM) .. ok
259: Add @SQ with -t (SAM -> BAM) .. ok
260: Add @SQ with -T (SAM -> BAM) .. ok
261: Add @SQ with -t (BAM -> BAM) .. ok
262: Add @SQ with -T (BAM -> BAM) .. ok
263: Add @SQ with -t (SAM -> CRAM) .. ok
264: Add @SQ with -T (SAM -> CRAM) .. ok
265: Add @SQ with -t (BAM -> CRAM) .. ok
266: Add @SQ with -T (BAM -> CRAM) .. ok
267: Make CRAM with no UR field .. ok
268: Decoding CRAM with no UR field via -T .. ok
269: CIGAR B-operator removal .. ok
270: Big SAM -> BAM .. ok
271: Big SAM -> BAM (2 threads) .. ok
272: Big SAM -> BAM (4 threads) .. ok
273: Big SAM -> CRAM .. ok
274: Big SAM -> CRAM (2 threads) .. ok
275: Big SAM -> CRAM (4 threads) .. ok
276: Subsample 0.2 (SAM input) ............ ok
277: Subsample 0.5 (SAM input) ............ ok
278: Subsample 0.8 (SAM input) ............ ok
279: Subsample 0.2 (BAM input) ............ ok
280: Subsample 0.5 (BAM input) ............ ok
281: Subsample 0.8 (BAM input) ............ ok
282: Subsample 0.2 (CRAM input) ............ ok
283: Subsample 0.5 (CRAM input) ............ ok
284: Subsample 0.8 (CRAM input) ............ ok
test_cat:
Generating test data file .................. done
Generate BAM file #1 .. ok
Generate CRAM file #1 .. ok
Generating test data file .................. done
Generate BAM file #2 .. ok
Generate CRAM file #2 .. ok
Generating test data file .................. done
Generate BAM file #3 .. ok
Generate CRAM file #3 .. ok
Generating test data file .................. done
Generate BAM file #4 .. ok
Generate CRAM file #4 .. ok
1: cat BAM files .. ok
2: cat recompressed BAM files .. ok
3: cat CRAM files .. ok
4: cat BAM files to stdout .. ok
5: cat recompressed BAM files to stdout .. ok
6: cat CRAM files to stdout .. ok
7: cat BAM files with new header .. ok
8: cat recompressed BAM files with new header .. ok
9: cat CRAM files with new header .. ok
test_bam2fq:
Generate BAM file .. ok
Generate CRAM file .. ok
1: fastq (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) [M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.002.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_depad:
Generate BAM file .. ok
depad (SAM input) .. ok
depad -s (SAM input) .. ok
depad -u (SAM input) .. ok
depad -1 (SAM input) .. ok
depad (BAM input) .. ok
depad -s (BAM input) .. ok
depad -u (BAM input) .. ok
depad -1 (BAM input) .. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/2_equal_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/3_map_cigar_equal_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/4_X_cigar_full_seq.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa -i 0 /<<PKGBUILDDIR>>/test/stat/5_insert_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/7_supp.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/8_secondary.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/1_map_cigar.sam | tail -n+4
.. ok
test_stats:
/<<PKGBUILDDIR>>/samtools stats -S RG -r /<<PKGBUILDDIR>>/test/stat/test.fa /<<PKGBUILDDIR>>/test/stat/10_map_cigar.sam | tail -n+4
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 -b /tmp/6aXj8B8Hjs - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -r -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_c.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -cp -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b.sam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_a_regex.sam /<<PKGBUILDDIR>>/test/dat/test_input_1_b_regex.sam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3LEoPPqrtz/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3LEoPPqrtz/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3LEoPPqrtz/sorttmp
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/1_coord_sort.sam -
ERR: [bam_mating_core] ERROR: Coordinate sorted, require grouped/sorted by queryname.
.. expected failure
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok
/<<PKGBUILDDIR>>/samtools calmd -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
test_idxstat:
/<<PKGBUILDDIR>>/samtools idxstats /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.truncated.cram
ERR:
.. expected failure
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -v /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.truncated.cram | sed 's,.*/quickcheck/,,'
The outputs stdout differ:
/<<PKGBUILDDIR>>/test/quickcheck/all.expected
/<<PKGBUILDDIR>>/test/quickcheck/all.expected.new
.. expected failure
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram && /<<PKGBUILDDIR>>/samtools view -h /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram && /<<PKGBUILDDIR>>/samtools view -h /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -R '1#7' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
Number of tests:
total .. 423
passed .. 403
failed .. 0
expected failure .. 20
unexpected pass .. 0
test/merge/test_bam_translate test/merge/test_bam_translate.tmp
test/merge/test_rtrans_build
test/merge/test_trans_tbl_init
cd test/mpileup && ./regression.sh mpileup.reg
=== Testing mpileup.reg regressions ===
Expected passes: 124
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
=== Testing depth.reg regressions ===
Expected passes: 14
Unexpected passes: 0
Expected failures: 0
Unexpected failures: 0
=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
rm -f debian/samtools.substvars
rm -f debian/samtools.*.debhelper
rm -rf debian/samtools/
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- \
prefix=/usr
install -d debian/samtools
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/usr
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p -m 755 /<<PKGBUILDDIR>>/debian/tmp/usr/bin /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p -m 644 samtools.1 misc/wgsim.1 /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f test/*.new test/*.tmp test/*/*.new test/*/*.tmp test/*/*.tmp.*
cd test/dat && rm -f test_input_*.bam.bai
cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth[12].bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim test/merge/test_bam_translate test/merge/test_rtrans_build test/merge/test_trans_tbl_init test/split/test_count_rg test/split/test_expand_format_string test/split/test_filter_header_rg test/split/test_parse_args test/vcf-miniview
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a -O--parallel
install -d debian/samtools//usr
cp --reflink=auto -a debian/tmp/usr/bin debian/samtools//usr/
install -d debian/samtools//usr/share/man
cp --reflink=auto -a debian/tmp/usr/share/man/man1 debian/samtools//usr/share/man/
cp --reflink=auto -a ./debian/mans/ace2sam.1 debian/samtools/usr/share/man/man1/
cp --reflink=auto -a ./debian/mans/samtools.pl.1 debian/samtools/usr/share/man/man1/
cp --reflink=auto -a ./debian/mans/wgsim.1 debian/samtools/usr/share/man/man1/
dh_installdocs -a -O--parallel
install -d debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a AUTHORS debian/samtools/usr/share/doc/samtools
cp --reflink=auto -a debian/reference debian/samtools/usr/share/doc/samtools
chown -R 0:0 debian/samtools/usr/share/doc
chmod -R go=rX debian/samtools/usr/share/doc
chmod -R u\+rw debian/samtools/usr/share/doc
install -p -m0644 debian/README.Debian debian/samtools/usr/share/doc/samtools/README.Debian
install -p -m0644 debian/copyright debian/samtools/usr/share/doc/samtools/copyright
dh_installchangelogs -a -O--parallel
install -p -m0644 debian/changelog debian/samtools/usr/share/doc/samtools/changelog.Debian
install -p -m0644 debian/NEWS debian/samtools/usr/share/doc/samtools/NEWS.Debian
dh_installman -a -O--parallel
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 644 samtools.1.new
mv -f samtools.1.new samtools.1
man --recode UTF-8 ./wgsim\.1 > wgsim\.1\.new
chmod 644 wgsim.1.new
mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
chmod 644 ace2sam.1.new
mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
chmod 644 samtools.pl.1.new
mv -f samtools.pl.1.new samtools.pl.1
dh_lintian -a -O--parallel
install -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl) > debian/samtools.substvars.new
mv debian/samtools.substvars.new debian/samtools.substvars
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
dh_compress -a -O--parallel
cd debian/samtools
chmod a-x usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
gzip -9nf usr/share/doc/samtools/NEWS.Debian usr/share/doc/samtools/changelog.Debian usr/share/man/man1/ace2sam.1 usr/share/man/man1/samtools.1 usr/share/man/man1/samtools.pl.1 usr/share/man/man1/wgsim.1
cd '/<<PKGBUILDDIR>>'
dh_fixperms -a -O--parallel
find debian/samtools -print0 2>/dev/null | xargs -0r chown --no-dereference 0:0
find debian/samtools ! -type l -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s
find debian/samtools/usr/share/doc -type f ! -regex 'debian/samtools/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/doc -type d -print0 2>/dev/null | xargs -0r chmod 0755
find debian/samtools/usr/share/man debian/samtools/usr/man/ debian/samtools/usr/X11*/man/ -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/include -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/share/applications -type f -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/lib/arm-linux-gnueabihf/perl5/5.22 debian/samtools/usr/share/perl5 -type f -perm -5 -name '*.pm' -print0 2>/dev/null | xargs -0r chmod a-X
find debian/samtools -perm -5 -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' \) -print0 2>/dev/null | xargs -0r chmod 0644
find debian/samtools/usr/bin -type f -print0 2>/dev/null | xargs -0r chmod a+x
find debian/samtools/usr/lib -type f -name '*.ali' -print0 2>/dev/null | xargs -0r chmod uga-w
find debian/samtools/usr/share/lintian/overrides -type f -print0 2>/dev/null | xargs -0r chmod 0644
dh_strip -a -O--parallel
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/3bc3f1c96de15a4a1213b8e6244fd7efc7f7db.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/3bc3f1c96de15a4a1213b8e6244fd7efc7f7db.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/samtools
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/ab/3bc3f1c96de15a4a1213b8e6244fd7efc7f7db.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/88
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/88/271fbf03fc2b40e118928fdf98eae20dedb407.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/88/271fbf03fc2b40e118928fdf98eae20dedb407.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/ace2sam
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/88/271fbf03fc2b40e118928fdf98eae20dedb407.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/254540783e3ec60a019c638dccd44c5a48d051.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/254540783e3ec60a019c638dccd44c5a48d051.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/254540783e3ec60a019c638dccd44c5a48d051.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/25
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/25/4d718a1cb4b2562649212f29263a0536bbdb21.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/25/4d718a1cb4b2562649212f29263a0536bbdb21.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-short
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/25/4d718a1cb4b2562649212f29263a0536bbdb21.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40/6b4651a0e54eabaf371685f3dd24a82671eeab.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40/6b4651a0e54eabaf371685f3dd24a82671eeab.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5fa
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/40/6b4651a0e54eabaf371685f3dd24a82671eeab.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/c8a91af870cdd742af6d994845f8d043bed91f.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/c8a91af870cdd742af6d994845f8d043bed91f.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/md5sum-lite
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/94/c8a91af870cdd742af6d994845f8d043bed91f.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/ebb20b76e600b40ea62b1437b24e4ea024da51.debug
chmod 0644 debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/ebb20b76e600b40ea62b1437b24e4ea024da51.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/wgsim
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/58/ebb20b76e600b40ea62b1437b24e4ea024da51.debug debian/samtools/usr/bin/wgsim
install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/samtools debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/wgsim
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa 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/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/md5fa were not linked against libdl.so.2 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -d debian/.debhelper/samtools/dbgsym-root/DEBIAN
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/.debhelper/samtools/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=extra -DAuto-Built-Package=debug-symbols -DPackage=samtools-dbgsym "-DDepends=samtools (= \${binary:Version})" "-DDescription=Debug symbols for samtools" "-DBuild-Ids=0c254540783e3ec60a019c638dccd44c5a48d051 254d718a1cb4b2562649212f29263a0536bbdb21 406b4651a0e54eabaf371685f3dd24a82671eeab 58ebb20b76e600b40ea62b1437b24e4ea024da51 88271fbf03fc2b40e118928fdf98eae20dedb407 94c8a91af870cdd742af6d994845f8d043bed91f ab3bc3f1c96de15a4a1213b8e6244fd7efc7f7db" -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/dbgsym-root/DEBIAN/control
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/control
dpkg-gencontrol -psamtools -ldebian/changelog -Tdebian/samtools.substvars -Pdebian/samtools
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: package samtools: unused substitution variable ${perl:Depends}
chmod 0644 debian/samtools/DEBIAN/control
chown 0:0 debian/samtools/DEBIAN/control
dh_md5sums -a -O--parallel
(cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/samtools/DEBIAN/md5sums
chown 0:0 debian/samtools/DEBIAN/md5sums
(cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum > DEBIAN/md5sums) >/dev/null
chmod 0644 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.3.1-1_armhf.deb'.
dpkg-deb --build debian/samtools ..
dpkg-deb: building package 'samtools' in '../samtools_1.3.1-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../samtools_1.3.1-1_armhf.changes
dpkg-genchanges: warning: package samtools-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.3.1
dpkg-source: info: using options from samtools-1.3.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160503-1452
Finished
--------
I: Built successfully
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| Changes |
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samtools_1.3.1-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 26 Apr 2016 21:12:05 +0900
Source: samtools
Binary: samtools samtools-test
Architecture: armhf
Version: 1.3.1-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Charles Plessy <plessy@debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Changes:
samtools (1.3.1-1) unstable; urgency=medium
.
0c961b2 Merge tag '1.3.1' into debian/unstable
3666b08 Conforms with Policy version 3.9.8.
Checksums-Sha1:
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1003d539df4d49b836953fd1767ea0a9b7b1aec9 219104 samtools_1.3.1-1_armhf.deb
Checksums-Sha256:
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d27d0036b414a1857a41160f868af191e488fd401d8368c72d5e937d3fae88b6 219104 samtools_1.3.1-1_armhf.deb
Files:
2b403c906f5d44d07e7def2323618cc4 453388 debug extra samtools-dbgsym_1.3.1-1_armhf.deb
9af4c2d0bfa712da8d914c224e533a6c 219104 science optional samtools_1.3.1-1_armhf.deb
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| Package contents |
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samtools-dbgsym_1.3.1-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 453388 bytes: control archive=820 bytes.
650 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 523
Depends: samtools (= 1.3.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Auto-Built-Package: debug-symbols
Build-Ids: 0c254540783e3ec60a019c638dccd44c5a48d051 254d718a1cb4b2562649212f29263a0536bbdb21 406b4651a0e54eabaf371685f3dd24a82671eeab 58ebb20b76e600b40ea62b1437b24e4ea024da51 88271fbf03fc2b40e118928fdf98eae20dedb407 94c8a91af870cdd742af6d994845f8d043bed91f ab3bc3f1c96de15a4a1213b8e6244fd7efc7f7db
drwxr-xr-x root/root 0 2016-05-03 14:51 ./
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 11108 2016-05-03 14:51 ./usr/lib/debug/.build-id/0c/254540783e3ec60a019c638dccd44c5a48d051.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root 11104 2016-05-03 14:51 ./usr/lib/debug/.build-id/25/4d718a1cb4b2562649212f29263a0536bbdb21.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/40/
-rw-r--r-- root/root 10988 2016-05-03 14:51 ./usr/lib/debug/.build-id/40/6b4651a0e54eabaf371685f3dd24a82671eeab.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/58/
-rw-r--r-- root/root 19340 2016-05-03 14:51 ./usr/lib/debug/.build-id/58/ebb20b76e600b40ea62b1437b24e4ea024da51.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/88/
-rw-r--r-- root/root 18816 2016-05-03 14:51 ./usr/lib/debug/.build-id/88/271fbf03fc2b40e118928fdf98eae20dedb407.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/94/
-rw-r--r-- root/root 8468 2016-05-03 14:51 ./usr/lib/debug/.build-id/94/c8a91af870cdd742af6d994845f8d043bed91f.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/lib/debug/.build-id/ab/
-rw-r--r-- root/root 436848 2016-05-03 14:51 ./usr/lib/debug/.build-id/ab/3bc3f1c96de15a4a1213b8e6244fd7efc7f7db.debug
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-05-03 14:51 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.3.1-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 219104 bytes: control archive=1639 bytes.
808 bytes, 17 lines control
1900 bytes, 32 lines md5sums
Package: samtools
Version: 1.3.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 639
Depends: libc6 (>= 2.7), libhts1 (>= 1.3), libncurses5 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3)
Recommends: python
Section: science
Priority: optional
Homepage: http://www.htslib.org/
Description: processing sequence alignments in SAM and BAM formats
Samtools is a set of utilities that manipulate nucleotide sequence alignments
in the binary BAM format. It imports from and exports to the ascii SAM
(Sequence Alignment/Map) format, does sorting, merging and indexing, and allows
one to retrieve reads in any regions swiftly. It is designed to work on a
stream, and is able to open a BAM (not SAM) file on a remote FTP or HTTP
server.
drwxr-xr-x root/root 0 2016-05-03 14:51 ./
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/bin/
-rwxr-xr-x root/root 17976 2016-05-03 14:51 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2016-04-22 09:22 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2016-04-22 09:22 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2016-04-22 09:22 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2016-04-22 09:22 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9772 2016-05-03 14:51 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9772 2016-05-03 14:51 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9788 2016-05-03 14:51 ./usr/bin/md5fa
-rwxr-xr-x root/root 5656 2016-05-03 14:51 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2016-04-22 09:22 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48367 2016-04-22 09:22 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2016-04-22 09:22 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2016-04-22 09:22 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 371264 2016-05-03 14:51 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2016-04-22 09:22 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2016-04-22 09:22 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2016-04-22 09:22 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2016-04-22 09:22 ./usr/bin/varfilter.py
-rwxr-xr-x root/root 18044 2016-05-03 14:51 ./usr/bin/wgsim
-rwxr-xr-x root/root 12540 2016-04-22 09:22 ./usr/bin/wgsim_eval.pl
-rwxr-xr-x root/root 3583 2016-04-22 09:22 ./usr/bin/zoom2sam.pl
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/doc/samtools/
-rw-r--r-- root/root 828 2016-04-22 09:22 ./usr/share/doc/samtools/AUTHORS
-rw-r--r-- root/root 295 2016-04-26 11:47 ./usr/share/doc/samtools/NEWS.Debian.gz
-rw-r--r-- root/root 721 2016-04-26 11:58 ./usr/share/doc/samtools/README.Debian
-rw-r--r-- root/root 3959 2016-04-26 12:12 ./usr/share/doc/samtools/changelog.Debian.gz
-rw-r--r-- root/root 2713 2016-04-26 11:47 ./usr/share/doc/samtools/copyright
-rw-r--r-- root/root 592 2016-04-26 11:47 ./usr/share/doc/samtools/reference
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/lintian/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 219 2016-04-26 11:47 ./usr/share/lintian/overrides/samtools
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/man/
drwxr-xr-x root/root 0 2016-05-03 14:51 ./usr/share/man/man1/
-rw-r--r-- root/root 462 2016-05-03 14:51 ./usr/share/man/man1/ace2sam.1.gz
-rw-r--r-- root/root 19456 2016-05-03 14:51 ./usr/share/man/man1/samtools.1.gz
-rw-r--r-- root/root 410 2016-05-03 14:51 ./usr/share/man/man1/samtools.pl.1.gz
-rw-r--r-- root/root 518 2016-05-03 14:51 ./usr/share/man/man1/wgsim.1.gz
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 16408
Build-Time: 531
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 299
Job: samtools_1.3.1-1
Machine Architecture: armhf
Package: samtools
Package-Time: 872
Source-Version: 1.3.1-1
Space: 16408
Status: successful
Version: 1.3.1-1
--------------------------------------------------------------------------------
Finished at 20160503-1452
Build needed 00:14:32, 16408k disc space