samtools →
1.4.1-1 →
armhf → 2017-07-29 08:03:30
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| samtools 1.4.1-1 (armhf) Sat, 29 Jul 2017 07:54:35 +0000 |
+==============================================================================+
Package: samtools
Version: 1.4.1-1
Source Version: 1.4.1-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-87bf6a90-51db-4f4b-83df-a139b5d12d8d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [11.9 MB]
Fetched 22.0 MB in 8s (2732 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 4012 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main samtools 1.4.1-1 (dsc) [2232 B]
Get:2 http://172.17.0.1/private buster-staging/main samtools 1.4.1-1 (tar) [3989 kB]
Get:3 http://172.17.0.1/private buster-staging/main samtools 1.4.1-1 (diff) [20.8 kB]
Fetched 4012 kB in 0s (6170 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/samtools-9K51t6/samtools-1.4.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/samtools-9K51t6' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-upXWR6/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-upXWR6/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-upXWR6/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (6135 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 772 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 772 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14837 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.4), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
Filtered Build-Depends: debhelper (>= 9), bash-completion, libio-pty-perl, libncurses5-dev, libhts-dev (>= 1.4), zlib1g-dev, automake, autoconf-archive, pkg-config, tabix (>= 1.0)
dpkg-deb: building package 'sbuild-build-depends-samtools-dummy' in '/<<BUILDDIR>>/resolver-upXWR6/apt_archive/sbuild-build-depends-samtools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-samtools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Sources [569 B]
Get:5 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ Packages [644 B]
Fetched 2546 B in 0s (6987 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install samtools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates openssl
Use 'apt autoremove' to remove them.
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 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts-dev libhts2 libicu57 libio-pty-perl libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1
libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config
po-debconf tabix zlib1g-dev
Suggested packages:
gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make
gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user
ncurses-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix 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 libfile-stripnondeterminism-perl libglib2.0-0
libgssapi-krb5-2 libhts-dev libhts2 libicu57 libio-pty-perl libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh2-1
libtimedate-perl libtinfo-dev libtool libxml2 m4 man-db pkg-config
po-debconf sbuild-build-depends-samtools-dummy tabix zlib1g-dev
0 upgraded, 54 newly installed, 0 to remove and 1 not upgraded.
Need to get 22.4 MB of archives.
After this operation, 79.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-upXWR6/apt_archive ./ sbuild-build-depends-samtools-dummy 0.invalid.0 [854 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf bash-completion all 1:2.1-4.3 [178 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf autoconf-archive all 20160916-1 [716 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.44+dfsg-8 [85.3 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-8 [195 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.2.5 [961 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.24.0-1 [70.4 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-5 [42.0 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libio-pty-perl armhf 1:1.08-1.1+b3 [32.9 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.0+20170715-2 [66.6 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.0+20170715-2 [246 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf tabix armhf 1.4.1-5 [249 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking gettext (0.19.8.1-2+b1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../37-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 .../38-po-debconf_1.0.20_all.deb ...
Unpacking po-debconf (1.0.20) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../39-debhelper_10.2.5_all.deb ...
Unpacking debhelper (10.2.5) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../40-libnghttp2-14_1.24.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.24.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../41-libpsl5_0.17.0-5_armhf.deb ...
Unpacking libpsl5:armhf (0.17.0-5) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../42-librtmp1_2.4+20151223.gitfa8646d.1-1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../43-libssh2-1_1.8.0-1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-1) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../44-libcurl3-gnutls_7.52.1-5_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.52.1-5) ...
Selecting previously unselected package libhts2:armhf.
Preparing to unpack .../45-libhts2_1.4.1-5_armhf.deb ...
Unpacking libhts2:armhf (1.4.1-5) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../46-libhts-dev_1.4.1-5_armhf.deb ...
Unpacking libhts-dev:armhf (1.4.1-5) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../47-libio-pty-perl_1%3a1.08-1.1+b3_armhf.deb ...
Unpacking libio-pty-perl (1:1.08-1.1+b3) ...
Selecting previously unselected package libtinfo-dev:armhf.
Preparing to unpack .../48-libtinfo-dev_6.0+20170715-2_armhf.deb ...
Unpacking libtinfo-dev:armhf (6.0+20170715-2) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../49-libncurses5-dev_6.0+20170715-2_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.0+20170715-2) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../50-pkg-config_0.29-4_armhf.deb ...
Unpacking pkg-config (0.29-4) ...
Selecting previously unselected package tabix.
Preparing to unpack .../51-tabix_1.4.1-5_armhf.deb ...
Unpacking tabix (1.4.1-5) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../52-zlib1g-dev_1%3a1.2.8.dfsg-5_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Selecting previously unselected package sbuild-build-depends-samtools-dummy.
Preparing to unpack .../53-sbuild-build-depends-samtools-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.24.0-1) ...
Setting up libio-pty-perl (1:1.08-1.1+b3) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libldap-common (2.4.44+dfsg-8) ...
Setting up libpsl5:armhf (0.17.0-5) ...
Setting up bash-completion (1:2.1-4.3) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.52.3-1) ...
No schema files found: doing nothing.
Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up libtinfo-dev:armhf (6.0+20170715-2) ...
Setting up gettext-base (0.19.8.1-2+b1) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-3) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libncurses5-dev:armhf (6.0+20170715-2) ...
Setting up pkg-config (0.29-4) ...
Setting up autoconf-archive (20160916-1) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.24-12) ...
Setting up autotools-dev (20161112.1) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-8) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 autopoint (0.19.8.1-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up gettext (0.19.8.1-2+b1) ...
Setting up autoconf (2.69-10) ...
Setting up file (1:5.30-1) ...
Setting up libkrb5support0:armhf (1.15.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-2) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.15.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libkrb5-3:armhf (1.15.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up libcurl3-gnutls:armhf (7.52.1-5) ...
Setting up tabix (1.4.1-5) ...
Setting up libhts2:armhf (1.4.1-5) ...
Setting up libhts-dev:armhf (1.4.1-5) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-samtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 autoconf_2.69-10 autoconf-archive_20160916-1 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 bash-completion_1:2.1-4.3 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libblkid1_2.29.2-2+rpi1 libbsd0_0.8.6-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3-gnutls_7.52.1-5 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libio-pty-perl_1:1.08-1.1+b3 libip4tc0_1.6.1-2 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.44+dfsg-8 libldap-common_2.4.44+dfsg-8 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncurses5-dev_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.24.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-5 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libsqlite3-0_3.19.3-3 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20170715-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libxml2_2.9.4+dfsg1-3 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 pkg-config_0.29-4 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-samtools-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tabix_1.4.1-5 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Jun 18 19:14:26 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./samtools_1.4.1-1.dsc
dpkg-source: info: extracting samtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking samtools_1.4.1.orig.tar.gz
dpkg-source: info: unpacking samtools_1.4.1-1.debian.tar.xz
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying literal_version.patch
dpkg-source: info: applying mayhem.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-87bf6a90-51db-4f4b-83df-a139b5d12d8d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package samtools
dpkg-buildpackage: info: source version 1.4.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build samtools-1.4.1
dpkg-buildpackage: info: host architecture armhf
dpkg-source: info: using options from samtools-1.4.1/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>>'
rm -f config.mk
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*.bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a libst.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 debian/ -I /usr/share/aclocal
configure.ac:45: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:45: the top level
autoconf
configure.ac:45: warning: AC_CONFIG_SUBDIRS: you should use literals
../../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:45: 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 Curses library... yes
checking for working curses.h... yes
checking for X/Open Enhanced Curses conformance... no
checking for Curses color functions... yes
checking for obsolete Curses functions... 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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedidx.o bedidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 "1.4.1"' > version.h
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2bcf.o bam2bcf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sample.o sample.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o phase.o phase.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam2depth.o bam2depth.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o padding.o padding.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bedcov.o bedcov.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bamshuf.o bamshuf.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o faidx.o faidx.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dict.o dict.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o stats.o stats.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bam.o bam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam.o sam.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -I. -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sam_utils.o sam_utils.c
gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -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')
ar -rcs libst.a sam_opts.o sam_utils.o
gcc -Wl,-z,relro -o misc/ace2sam misc/ace2sam.o -lz
gcc -Wl,-z,relro -o misc/maq2sam-long misc/maq2sam-long.o -lz
gcc -Wl,-z,relro -o misc/maq2sam-short misc/maq2sam-short.o -lz
gcc -Wl,-z,relro -o misc/md5fa misc/md5fa.o -lhts -lz
gcc -Wl,-z,relro -o misc/md5sum-lite misc/md5sum-lite.o -lhts -lz
gcc -Wl,-z,relro -o misc/wgsim misc/wgsim.o -lm -lz
gcc -Wl,-z,relro -o test/merge/test_bam_translate test/merge/test_bam_translate.o test/test.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/merge/test_rtrans_build test/merge/test_rtrans_build.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/split/test_count_rg test/split/test_count_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/split/test_expand_format_string test/split/test_expand_format_string.o test/test.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/split/test_filter_header_rg test/split/test_filter_header_rg.o test/test.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/split/test_parse_args test/split/test_parse_args.o test/test.o libst.a -lhts -lz -lpthread
gcc -Wl,-z,relro -o test/vcf-miniview test/vcf-miniview.o -lhts -lz -lpthread
gcc -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 bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o bam2bcf_indel.o sample.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 libst.a -lhts -lcurses -lm -lz -lpthread
gcc -Wl,-z,relro -o test/merge/test_trans_tbl_init test/merge/test_trans_tbl_init.o libst.a -lhts -lz -lpthread
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/3htbt_zkFb/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 979200 -s 6 /tmp/3htbt_zkFb/bgzip.dat.gz
.. ok
/usr/bin/bgzip -c -b 652804 -s 6 /tmp/3htbt_zkFb/bgzip.dat.gz
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa.gz 3:11-13 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa.gz 2:998-1003 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa.gz 1:100-104 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/faidx.fa 1:99998-100007 | grep -v '^>'
.. ok
/<<PKGBUILDDIR>>/samtools faidx /tmp/3htbt_zkFb/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/3htbt_zkFb/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 view /tmp/3htbt_zkFb/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view /tmp/3htbt_zkFb/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_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/3htbt_zkFb/large_chrom.bam ref2
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools view -@ 2 /tmp/3htbt_zkFb/large_chrom.bam ref2:1-541556283
.. ok
test_index:
/<<PKGBUILDDIR>>/samtools index -@ 2 /<<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/3htbt_zkFb/mpileup.bam.list -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/3htbt_zkFb/mpileup.cram.list -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/3htbt_zkFb/mpileup.bam.urllist -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -b /tmp/3htbt_zkFb/mpileup.cram.urllist -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-150
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/3htbt_zkFb/mpileup.bam.list -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -uvDV -b /tmp/3htbt_zkFb/mpileup.cram.list -f /tmp/3htbt_zkFb/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/3htbt_zkFb/mpileup.cram.list -f /tmp/3htbt_zkFb/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/3htbt_zkFb/mpileup.cram.list -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:100-600| grep -v ^##samtools | grep -v ^##ref
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:1050-1060 /tmp/3htbt_zkFb/mpileup.1.bam | grep -v mpileup
.. ok
test_mpileup:
/<<PKGBUILDDIR>>/samtools mpileup -B --ff 0x14 -f /tmp/3htbt_zkFb/mpileup.ref.fa.gz -r17:1050-1060 /tmp/3htbt_zkFb/mpileup.1.cram | grep -v mpileup
IO::Tty::pty_allocate(nonfatal): grantpt(): Operation not permitted at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
IO::Tty::open_slave(nonfatal): open(/dev/pts/0): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
pty_allocate(nonfatal): posix_openpt(): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
IO::Tty::pty_allocate(nonfatal): grantpt(): Operation not permitted at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
IO::Tty::open_slave(nonfatal): open(/dev/pts/0): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
pty_allocate(nonfatal): getpt(): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
pty_allocate(nonfatal): openpty(): Operation not permitted at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
IO::Tty::pty_allocate(nonfatal): grantpt(): Operation not permitted at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
IO::Tty::open_slave(nonfatal): open(/dev/pts/0): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
pty_allocate(nonfatal): open(/dev/ptmx): Permission denied at /usr/lib/arm-linux-gnueabihf/perl5/5.26/IO/Pty.pm line 24.
test/test.pl: no IO::Pty module or can't open pty; skipping usage tests
.. ok
test_usage:
samtools
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/3htbt_zkFb/view.001.fogn (SAM input) .. ok
50: Count -R /tmp/3htbt_zkFb/view.001.fogn (SAM input) .. ok
51: Filter -R /tmp/3htbt_zkFb/view.001.fogn (BAM input) .. ok
52: Count -R /tmp/3htbt_zkFb/view.001.fogn (BAM input) .. ok
53: Filter -R /tmp/3htbt_zkFb/view.001.fogn (CRAM input) .. ok
54: Count -R /tmp/3htbt_zkFb/view.001.fogn (CRAM input) .. ok
55: Filter -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (SAM input).. ok
56: Count -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (SAM input).. ok
57: Filter -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (BAM input).. ok
58: Count -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (BAM input).. ok
59: Filter -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (CRAM input).. ok
60: Count -R /tmp/3htbt_zkFb/view.001.fogn -r grp2 (CRAM input).. ok
61: Filter -r grp2 -R /tmp/3htbt_zkFb/view.001.fogn (SAM input).. ok
62: Count -r grp2 -R /tmp/3htbt_zkFb/view.001.fogn (SAM input).. ok
63: Filter -r grp2 -R /tmp/3htbt_zkFb/view.001.fogn (BAM input).. ok
64: Count -r grp2 -R /tmp/3htbt_zkFb/view.001.fogn (BAM input).. ok
65: Filter -r grp2 -R /tmp/3htbt_zkFb/view.001.fogn (CRAM input).. ok
66: Count -r grp2 -R /tmp/3htbt_zkFb/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 * (BAM input) .. ok
199: Count * (BAM input) .. ok
200: Region * (CRAM input) .. ok
201: Count * (CRAM input) .. ok
202: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
203: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (BAM input).. ok
204: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
205: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed (CRAM input).. ok
206: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
207: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (BAM input).. ok
208: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
209: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.02.bed (CRAM input).. ok
210: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
211: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (BAM input).. ok
212: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
213: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed (CRAM input).. ok
214: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
215: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (BAM input).. ok
216: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
217: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.02.bed (CRAM input).. ok
218: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
219: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (BAM input).. ok
220: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
221: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z (CRAM input).. ok
222: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
223: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (BAM input).. ok
224: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
225: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:30 (CRAM input).. ok
226: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
227: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (BAM input).. ok
228: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
229: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:10-30 (CRAM input).. ok
230: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
231: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (BAM input).. ok
232: Region -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
233: Count -L /<<PKGBUILDDIR>>/test/dat/view.002.01.bed Z:25-35 (CRAM input).. ok
234: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
235: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (BAM input).. ok
236: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
237: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref1:11-16 (CRAM input).. ok
238: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
239: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (BAM input).. ok
240: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
241: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed ref2 (CRAM input).. ok
242: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
243: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (BAM input).. ok
244: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
245: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 (CRAM input).. ok
246: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
247: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (BAM input).. ok
248: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
249: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -f 128 (CRAM input).. ok
250: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
251: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (BAM input).. ok
252: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
253: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -q 5 (CRAM input).. ok
254: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
255: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (BAM input).. ok
256: Region -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
257: Count -L /<<PKGBUILDDIR>>/test/dat/view.001.01.bed -r grp1 ref1:11-16 (CRAM input).. ok
258: Make BAM with no M5/UR tags .. ok
259: Add @SQ with -t (SAM -> SAM) .. ok
260: Add @SQ with -T (SAM -> SAM) .. ok
261: Add @SQ with -t (BAM -> SAM) .. ok
262: Add @SQ with -T (BAM -> SAM) .. ok
263: Add @SQ with -t (SAM -> BAM) .. ok
264: Add @SQ with -T (SAM -> BAM) .. ok
265: Add @SQ with -t (BAM -> BAM) .. ok
266: Add @SQ with -T (BAM -> BAM) .. ok
267: Add @SQ with -t (SAM -> CRAM) .. ok
268: Add @SQ with -T (SAM -> CRAM) .. ok
269: Add @SQ with -t (BAM -> CRAM) .. ok
270: Add @SQ with -T (BAM -> CRAM) .. ok
271: Make CRAM with no UR field .. ok
272: Decoding CRAM with no UR field via -T .. ok
273: CIGAR B-operator removal .. ok
274: Big SAM -> BAM .. ok
275: Big SAM -> BAM (2 threads) .. ok
276: Big SAM -> BAM (4 threads) .. ok
277: Big SAM -> CRAM .. ok
278: Big SAM -> CRAM (2 threads) .. ok
279: Big SAM -> CRAM (4 threads) .. ok
280: Subsample 0.2 (SAM input) ............ ok
281: Subsample 0.5 (SAM input) ............ ok
282: Subsample 0.8 (SAM input) ............ ok
283: Subsample 0.2 (BAM input) ............ ok
284: Subsample 0.5 (BAM input) ............ ok
285: Subsample 0.8 (BAM input) ............ ok
286: Subsample 0.2 (CRAM input) ............ ok
287: Subsample 0.5 (CRAM input) ............ ok
288: 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_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.sam
.. ok
test_bam2fq:
Generate BAM file (2 threads) .. ok
Generate CRAM file (2 threads) .. ok
1: fastq (SAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
2: fastq -n (SAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
3: fastq (BAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
4: fastq -n (BAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
5: fastq (CRAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
6: fastq -n (CRAM input) (2 threads) [M::bam2fq_mainloop] processed 36 reads
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.001.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 -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 -@ 2 -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 -@ 2 -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.003.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC --index-format 'n2i2' --i1 /<<PKGBUILDDIR>>/test/bc.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.004.sam
.. ok
test_bam2fq:
/<<PKGBUILDDIR>>/samtools fastq -@ 2 --barcode-tag BC -N --index-format 'n*i*' --i1 /<<PKGBUILDDIR>>/test/bc_split.fq -s /<<PKGBUILDDIR>>/test/s.fq -1 /<<PKGBUILDDIR>>/test/1.fq -2 /<<PKGBUILDDIR>>/test/2.fq /<<PKGBUILDDIR>>/test/dat/bam2fq.005.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/r56XtL7PDu - /<<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_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -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 -@ 2 -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 -@ 2 -s 1 -b /tmp/ghntPDvb1g - /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -s 1 - /<<PKGBUILDDIR>>/test/dat/test_input_1_b.bam
.. ok
test_merge:
/<<PKGBUILDDIR>>/samtools merge -@ 2 -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 -@ 2 -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 -@ 2 -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/3htbt_zkFb/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3htbt_zkFb/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3htbt_zkFb/sorttmp
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3htbt_zkFb/sortout
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -f /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3htbt_zkFb/sortout.bam
.. ok
test_sort:
/<<PKGBUILDDIR>>/samtools sort -@ 2 -o /<<PKGBUILDDIR>>/test/dat/test_input_1_a.bam /tmp/3htbt_zkFb/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
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -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 -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/2_isize_overflow.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/3_reverse_read_pp_lt.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/4_reverse_read_pp_equal.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/5_ct.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -cO sam /<<PKGBUILDDIR>>/test/fixmate/6_ct_replace.sam -
.. ok
test_fixmate:
/<<PKGBUILDDIR>>/samtools fixmate -@ 2 -O sam /<<PKGBUILDDIR>>/test/fixmate/7_two_read_mapped.sam -
.. ok
/<<PKGBUILDDIR>>/samtools calmd -uAr /<<PKGBUILDDIR>>/test/dat/mpileup.1.sam /<<PKGBUILDDIR>>/test/dat/mpileup.ref.fa
.. ok
/<<PKGBUILDDIR>>/samtools calmd -@ 2 -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.scramble30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram
.. ok
test_quickcheck:
/<<PKGBUILDDIR>>/samtools quickcheck -v /<<PKGBUILDDIR>>/test/quickcheck/1.quickcheck.badeof.bam /<<PKGBUILDDIR>>/test/quickcheck/2.quickcheck.badheader.bam /<<PKGBUILDDIR>>/test/quickcheck/3.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/4.quickcheck.ok.bam /<<PKGBUILDDIR>>/test/quickcheck/5.quickcheck.scramble30.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/6.quickcheck.cram21.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/7.quickcheck.cram30.ok.cram /<<PKGBUILDDIR>>/test/quickcheck/8.quickcheck.cram21.truncated.cram /<<PKGBUILDDIR>>/test/quickcheck/9.quickcheck.cram30.truncated.cram | sed 's,.*/quickcheck/,,'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.bam | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | /<<PKGBUILDDIR>>/samtools view -h | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram && /<<PKGBUILDDIR>>/samtools view -h /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v21.cram | perl -pe 's/ VN:.*//'
.. ok
test_reheader:
/<<PKGBUILDDIR>>/samtools reheader --in-place /<<PKGBUILDDIR>>/test/reheader/hdr.sam /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram && /<<PKGBUILDDIR>>/samtools view -h /<<PKGBUILDDIR>>/test/dat/view.001.tmp.v30.cram | perl -pe 's/ VN:.*//'
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -R '1#7' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m orphan_only /<<PKGBUILDDIR>>/test/addrprg/2_fixup_orphan.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -R '1#7' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r '@RG\tID:1#8\tCN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -m overwrite_all -R '1#8' /<<PKGBUILDDIR>>/test/addrprg/1_fixup.sam
.. ok
test_addrprg:
/<<PKGBUILDDIR>>/samtools addreplacerg -@ 2 -O sam -r 'ID:1#8' -r 'CN:SC' /<<PKGBUILDDIR>>/test/addrprg/4_fixup_norg.sam
.. ok
Number of tests:
total .. 447
passed .. 445
failed .. 0
expected failure .. 2
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 FAIL: Task failed, but expected to fail;
when running $samtools mpileup -Q0 -x -f c1.fa c1#pad1.bam
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -Q0 -x -f c1.fa c1#pad2.bam
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools mpileup -ABQ0 -a -l xx.bed3 xx#depth3.bam
Expected passes: 153
Unexpected passes: 0
Expected failures: 3
Unexpected failures: 0
=> PASS
cd test/mpileup && ./regression.sh depth.reg
=== Testing depth.reg regressions ===
EXPECTED FAIL: Task failed, but expected to fail;
when running $samtools depth -a -b xx.bed3 xx#depth3.bam
Expected passes: 43
Unexpected passes: 0
Expected failures: 1
Unexpected failures: 0
=> PASS
test/split/test_count_rg
test/split/test_expand_format_string
test/split/test_filter_header_rg
test/split/test_parse_args
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --parallel
create-stamp debian/debhelper-build-stamp
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/bin /<<PKGBUILDDIR>>/debian/tmp/usr/share/man/man1
install -p samtools /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p misc/ace2sam misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /<<PKGBUILDDIR>>/debian/tmp/usr/bin
install -p 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*.bam*
rm -f *.o misc/*.o test/*.o test/*/*.o version.h
rm -f samtools libbam.a libst.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/
install -d debian/samtools/usr/share/commonwl/
cp --reflink=auto -a ./debian/samtools-faidx.cwl debian/samtools/usr/share/commonwl//
cp --reflink=auto -a ./debian/samtools-index.cwl debian/samtools/usr/share/commonwl//
cp --reflink=auto -a ./debian/samtools-rmdup.cwl debian/samtools/usr/share/commonwl//
cp --reflink=auto -a ./debian/samtools-sort.cwl debian/samtools/usr/share/commonwl//
cp --reflink=auto -a ./debian/samtools-view.cwl debian/samtools/usr/share/commonwl//
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 ./wgsim\.1 > wgsim\.1\.new
chmod 0755 -- wgsim.1.new
chown 0:0 -- wgsim.1.new
mv -f wgsim.1.new wgsim.1
man --recode UTF-8 ./ace2sam\.1 > ace2sam\.1\.new
chmod 0755 -- ace2sam.1.new
chown 0:0 -- ace2sam.1.new
mv -f ace2sam.1.new ace2sam.1
man --recode UTF-8 ./samtools\.pl\.1 > samtools\.pl\.1\.new
chmod 0755 -- samtools.pl.1.new
chown 0:0 -- samtools.pl.1.new
mv -f samtools.pl.1.new samtools.pl.1
man --recode UTF-8 ./samtools\.1 > samtools\.1\.new
chmod 0755 -- samtools.1.new
chown 0:0 -- samtools.1.new
mv -f samtools.1.new samtools.1
dh_lintian -a -O--parallel
install -d debian/samtools/usr/share/lintian/overrides
install -p -m0644 debian/samtools.lintian-overrides debian/samtools/usr/share/lintian/overrides/samtools
dh_perl -a -O--parallel
(grep -a -s -v perl:Depends debian/samtools.substvars; echo perl:Depends=perl:any) > 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 -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/perl5/5.26 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/44
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/wgsim debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/2ac9d4873ed33cddd29b49e76232e7d0ec5405.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/2ac9d4873ed33cddd29b49e76232e7d0ec5405.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/44/2ac9d4873ed33cddd29b49e76232e7d0ec5405.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/44/2ac9d4873ed33cddd29b49e76232e7d0ec5405.debug debian/samtools/usr/bin/wgsim
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-short debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/633d3e6660a04ec4cd5ef63f6c8888870e3bef.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/633d3e6660a04ec4cd5ef63f6c8888870e3bef.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/0c/633d3e6660a04ec4cd5ef63f6c8888870e3bef.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/0c/633d3e6660a04ec4cd5ef63f6c8888870e3bef.debug debian/samtools/usr/bin/maq2sam-short
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dc
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/ace2sam debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dc/779206fa3c9656ba3d997bc3466bae46ee01b3.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dc/779206fa3c9656ba3d997bc3466bae46ee01b3.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/dc/779206fa3c9656ba3d997bc3466bae46ee01b3.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/dc/779206fa3c9656ba3d997bc3466bae46ee01b3.debug debian/samtools/usr/bin/ace2sam
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/maq2sam-long debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/ddae8aff6265f27396af6ee9c0982385a26f82.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/ddae8aff6265f27396af6ee9c0982385a26f82.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/ddae8aff6265f27396af6ee9c0982385a26f82.debug
strip --remove-section=.comment --remove-section=.note debian/samtools/usr/bin/maq2sam-long
objcopy --add-gnu-debuglink debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/e2/ddae8aff6265f27396af6ee9c0982385a26f82.debug debian/samtools/usr/bin/maq2sam-long
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/samtools debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9539ab6eb2e4201f493ec09b144742ba1a2b18.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9539ab6eb2e4201f493ec09b144742ba1a2b18.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/5d/9539ab6eb2e4201f493ec09b144742ba1a2b18.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/5d/9539ab6eb2e4201f493ec09b144742ba1a2b18.debug debian/samtools/usr/bin/samtools
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5fa debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/94f9a24cb0bd880f9fe5160e394480ea7a5960.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/94f9a24cb0bd880f9fe5160e394480ea7a5960.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/46/94f9a24cb0bd880f9fe5160e394480ea7a5960.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/46/94f9a24cb0bd880f9fe5160e394480ea7a5960.debug debian/samtools/usr/bin/md5fa
install -d debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47
objcopy --only-keep-debug --compress-debug-sections debian/samtools/usr/bin/md5sum-lite debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/0e2d6de3de92606d68ede3902822a65aa23600.debug
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/0e2d6de3de92606d68ede3902822a65aa23600.debug
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/usr/lib/debug/.build-id/47/0e2d6de3de92606d68ede3902822a65aa23600.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/47/0e2d6de3de92606d68ede3902822a65aa23600.debug debian/samtools/usr/bin/md5sum-lite
install -d debian/.debhelper/samtools/dbgsym-root/usr/share/doc
ln -s samtools debian/.debhelper/samtools/dbgsym-root/usr/share/doc/samtools-dbgsym
dh_makeshlibs -a -O--parallel
rm -f debian/samtools/DEBIAN/shlibs
dh_shlibdeps -a -O--parallel
install -d debian/samtools/DEBIAN
dpkg-shlibdeps -Tdebian/samtools.substvars debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa debian/samtools/usr/bin/md5sum-lite
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/samtools/usr/bin/ace2sam debian/samtools/usr/bin/maq2sam-long debian/samtools/usr/bin/maq2sam-short debian/samtools/usr/bin/wgsim debian/samtools/usr/bin/md5sum-lite debian/samtools/usr/bin/samtools debian/samtools/usr/bin/md5fa were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
echo misc:Depends= >> debian/samtools.substvars
echo misc:Pre-Depends= >> debian/samtools.substvars
install -d debian/.debhelper/samtools/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=0c633d3e6660a04ec4cd5ef63f6c8888870e3bef 442ac9d4873ed33cddd29b49e76232e7d0ec5405 4694f9a24cb0bd880f9fe5160e394480ea7a5960 470e2d6de3de92606d68ede3902822a65aa23600 5d9539ab6eb2e4201f493ec09b144742ba1a2b18 dc779206fa3c9656ba3d997bc3466bae46ee01b3 e2ddae8aff6265f27396af6ee9c0982385a26f82" -DSection=debug -UMulti-Arch -UReplaces -UBreaks
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: package samtools: unused substitution variable ${perl:Depends}
chmod 0644 -- debian/samtools/DEBIAN/control
chown 0:0 -- debian/samtools/DEBIAN/control
dh_md5sums -a -O--parallel
(cd debian/samtools >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/samtools/DEBIAN/md5sums
chown 0:0 -- debian/samtools/DEBIAN/md5sums
(cd debian/.debhelper/samtools/dbgsym-root >/dev/null ; find . -type f ! -regex './DEBIAN/.*' -printf '%P\0' | LC_ALL=C sort -z | xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums) >/dev/null
chmod 0644 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
chown 0:0 -- debian/.debhelper/samtools/dbgsym-root/DEBIAN/md5sums
dh_builddeb -a -O--parallel
dpkg-deb -z1 -Zxz -Sextreme --build debian/.debhelper/samtools/dbgsym-root ..
dpkg-deb: building package 'samtools-dbgsym' in '../samtools-dbgsym_1.4.1-1_armhf.deb'.
dpkg-deb --build debian/samtools ..
dpkg-deb: building package 'samtools' in '../samtools_1.4.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../samtools_1.4.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build samtools-1.4.1
dpkg-source: info: using options from samtools-1.4.1/debian/source/options: --single-debian-patch --extend-diff-ignore=^(\.travis.*|README.md)$
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-07-29T08:03:27Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
samtools_1.4.1-1_armhf.changes:
-------------------------------
Format: 1.8
Date: Sun, 18 Jun 2017 21:11:09 +0200
Source: samtools
Binary: samtools samtools-test
Architecture: armhf
Version: 1.4.1-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
samtools - processing sequence alignments in SAM and BAM formats
samtools-test - test files for the samtools package
Closes: 865008
Changes:
samtools (1.4.1-1) unstable; urgency=medium
.
* New upstream version
Closes: #865008
Checksums-Sha1:
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60ae03a56dbdf1555fb0a7ea138d565e99f1ba56 5336 samtools_1.4.1-1_armhf.buildinfo
4fc18c63ed8c0bfaebd41f797db27b40fa744819 218234 samtools_1.4.1-1_armhf.deb
Checksums-Sha256:
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bc1ba7b671197880db0148914d2535fab0e10c5eabb14255b4f49e052c3f84ba 5336 samtools_1.4.1-1_armhf.buildinfo
e31929da7c46768ad75bbaa0187a932cfc742e4fe71fc340f4ede7c97fe2fe0b 218234 samtools_1.4.1-1_armhf.deb
Files:
33ea6305cf7bc68ff09054f139d1db93 467434 debug extra samtools-dbgsym_1.4.1-1_armhf.deb
65edd7cf51f8ee5bfff881e46f9ac5b7 5336 science optional samtools_1.4.1-1_armhf.buildinfo
0b88376365a1ac00371d0d34e3ddf9ab 218234 science optional samtools_1.4.1-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
samtools-dbgsym_1.4.1-1_armhf.deb
---------------------------------
new debian package, version 2.0.
size 467434 bytes: control archive=813 bytes.
650 bytes, 13 lines control
742 bytes, 7 lines md5sums
Package: samtools-dbgsym
Source: samtools
Version: 1.4.1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 539
Depends: samtools (= 1.4.1-1)
Section: debug
Priority: extra
Homepage: http://www.htslib.org/
Description: Debug symbols for samtools
Build-Ids: 0c633d3e6660a04ec4cd5ef63f6c8888870e3bef 442ac9d4873ed33cddd29b49e76232e7d0ec5405 4694f9a24cb0bd880f9fe5160e394480ea7a5960 470e2d6de3de92606d68ede3902822a65aa23600 5d9539ab6eb2e4201f493ec09b144742ba1a2b18 dc779206fa3c9656ba3d997bc3466bae46ee01b3 e2ddae8aff6265f27396af6ee9c0982385a26f82
drwxr-xr-x root/root 0 2017-06-18 19:11 ./
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 11480 2017-06-18 19:11 ./usr/lib/debug/.build-id/0c/633d3e6660a04ec4cd5ef63f6c8888870e3bef.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 19900 2017-06-18 19:11 ./usr/lib/debug/.build-id/44/2ac9d4873ed33cddd29b49e76232e7d0ec5405.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/46/
-rw-r--r-- root/root 11328 2017-06-18 19:11 ./usr/lib/debug/.build-id/46/94f9a24cb0bd880f9fe5160e394480ea7a5960.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/47/
-rw-r--r-- root/root 8728 2017-06-18 19:11 ./usr/lib/debug/.build-id/47/0e2d6de3de92606d68ede3902822a65aa23600.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root 447076 2017-06-18 19:11 ./usr/lib/debug/.build-id/5d/9539ab6eb2e4201f493ec09b144742ba1a2b18.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/dc/
-rw-r--r-- root/root 21092 2017-06-18 19:11 ./usr/lib/debug/.build-id/dc/779206fa3c9656ba3d997bc3466bae46ee01b3.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/lib/debug/.build-id/e2/
-rw-r--r-- root/root 11484 2017-06-18 19:11 ./usr/lib/debug/.build-id/e2/ddae8aff6265f27396af6ee9c0982385a26f82.debug
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/share/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-06-18 19:11 ./usr/share/doc/samtools-dbgsym -> samtools
samtools_1.4.1-1_armhf.deb
--------------------------
new debian package, version 2.0.
size 218234 bytes: control archive=1782 bytes.
799 bytes, 17 lines control
2258 bytes, 37 lines md5sums
Package: samtools
Version: 1.4.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 648
Depends: libc6 (>= 2.7), libhts2, 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 2017-06-18 19:11 ./
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/
drwxr-xr-x root/root 0 2017-06-18 19:11 ./usr/bin/
-rwxr-xr-x root/root 18028 2017-06-18 19:11 ./usr/bin/ace2sam
-rwxr-xr-x root/root 5328 2017-05-08 10:07 ./usr/bin/blast2sam.pl
-rwxr-xr-x root/root 3364 2017-05-08 10:07 ./usr/bin/bowtie2sam.pl
-rwxr-xr-x root/root 18032 2017-05-08 10:07 ./usr/bin/export2sam.pl
-rwxr-xr-x root/root 6125 2017-05-08 10:07 ./usr/bin/interpolate_sam.pl
-rwxr-xr-x root/root 9824 2017-06-18 19:11 ./usr/bin/maq2sam-long
-rwxr-xr-x root/root 9824 2017-06-18 19:11 ./usr/bin/maq2sam-short
-rwxr-xr-x root/root 9840 2017-06-18 19:11 ./usr/bin/md5fa
-rwxr-xr-x root/root 5708 2017-06-18 19:11 ./usr/bin/md5sum-lite
-rwxr-xr-x root/root 6773 2017-05-08 10:07 ./usr/bin/novo2sam.pl
-rwxr-xr-x root/root 48659 2017-05-08 10:07 ./usr/bin/plot-bamstats
-rwxr-xr-x root/root 3208 2017-05-08 10:07 ./usr/bin/psl2sam.pl
-rwxr-xr-x root/root 8961 2017-05-08 10:07 ./usr/bin/sam2vcf.pl
-rwxr-xr-x root/root 359016 2017-06-18 19:11 ./usr/bin/samtools
-rwxr-xr-x root/root 16478 2017-05-08 10:07 ./usr/bin/samtools.pl
-rwxr-xr-x root/root 11105 2017-05-08 10:07 ./usr/bin/seq_cache_populate.pl
-rwxr-xr-x root/root 3909 2017-05-08 10:07 ./usr/bin/soap2sam.pl
-rwxr-xr-x root/root 7888 2017-05-08 10:07 ./usr/bin/varfilter.py
-rwxr-xr-x root/root 18096 2017-06-18 19:11 ./usr/bin/wgsim
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 17588
Build-Time: 216
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 298
Job: samtools_1.4.1-1
Machine Architecture: armhf
Package: samtools
Package-Time: 532
Source-Version: 1.4.1-1
Space: 17588
Status: successful
Version: 1.4.1-1
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Finished at 2017-07-29T08:03:27Z
Build needed 00:08:52, 17588k disk space