seqprep →
1.1-6 →
armhf → 2016-03-29 11:25:44
sbuild (Debian sbuild) 0.68.0 (15 Jan 2016) on bm-wb-01
+==============================================================================+
| seqprep 1.1-6 (armhf) 29 Mar 2016 11:13 |
+==============================================================================+
Package: seqprep
Version: 1.1-6
Source Version: 1.1-6
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/seqprep-bnClsS/seqprep-1.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/seqprep-bnClsS' with '<<BUILDDIR>>'
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/stretch-staging-armhf-sbuild-1a6e1942-40ed-43af-9ece-31059339542d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [8849 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [10.9 MB]
Fetched 19.8 MB in 24s (809 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'seqprep' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/seqprep/trunk/
Need to get 37.2 MB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main seqprep 1.1-6 (dsc) [2084 B]
Get:2 http://172.17.0.1/private stretch-staging/main seqprep 1.1-6 (tar) [37.2 MB]
Get:3 http://172.17.0.1/private stretch-staging/main seqprep 1.1-6 (diff) [9172 B]
Fetched 37.2 MB in 3s (9650 kB/s)
Download complete and in download only mode
+------------------------------------------------------------------------------+
| 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-Kk7spF/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Packages [526 B]
Ign:4 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Sources [214 B]
Get:5 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ Packages [526 B]
Reading package lists...
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 37 not upgraded.
Need to get 0 B/768 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-Kk7spF/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [768 B]
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sbuild-build-depends-core-dummy.
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(Reading database ... 12614 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), python, python-markdown, ruby-ronn, zlib1g-dev
Filtered Build-Depends: debhelper (>= 9), python, python-markdown, ruby-ronn, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-seqprep-dummy' in '/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive/sbuild-build-depends-seqprep-dummy.deb'.
OK
Get:1 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ InRelease
Ign:1 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Release [2119 B]
Get:2 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Release [2119 B]
Get:3 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Release.gpg [299 B]
Get:3 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Release.gpg [299 B]
Get:4 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Sources [237 B]
Get:5 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Packages [557 B]
Ign:4 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Sources
Ign:5 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Packages
Get:4 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Sources [237 B]
Get:5 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ Packages [557 B]
Reading package lists...
Reading package lists...
Install seqprep build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
manpages
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autotools-dev bsdmainutils ca-certificates debhelper dh-strip-nondeterminism
file gettext gettext-base groff groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libexpat1 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libice6 libicu55 libmagic1
libmarkdown2 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libruby2.3 libsm6 libsqlite3-0 libssl1.0.2
libtimedate-perl libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1
libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 libyaml-0-2 man-db
mime-support openssl po-debconf python python-markdown python-minimal
python2.7 python2.7-minimal rake ruby ruby-did-you-mean ruby-fast-xs
ruby-hpricot ruby-minitest ruby-mustache ruby-net-telnet ruby-power-assert
ruby-rdiscount ruby-ronn ruby-test-unit ruby2.3 rubygems-integration
x11-common zlib1g-dev
Suggested packages:
wamerican | wordlist whois vacation dh-make gettext-doc autopoint
libasprintf-dev libgettextpo-dev less www-browser libmail-box-perl
python-doc python-tk python-markdown-doc python2.7-doc binfmt-support ri
ruby-dev bundler
Recommended packages:
curl | wget | lynx-cur ghostscript imagemagick libpaper1 netpbm psutils
libglib2.0-data shared-mime-info xdg-user-dirs xml-core
libmail-sendmail-perl python-pygments python-yaml zip fonts-lato
libjs-jquery
The following NEW packages will be installed:
autotools-dev bsdmainutils ca-certificates debhelper dh-strip-nondeterminism
file gettext gettext-base groff groff-base intltool-debian
libarchive-zip-perl libbsd0 libcroco3 libexpat1 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libice6 libicu55 libmagic1
libmarkdown2 libpipeline1 libpython-stdlib libpython2.7-minimal
libpython2.7-stdlib libruby2.3 libsm6 libsqlite3-0 libssl1.0.2
libtimedate-perl libunistring0 libx11-6 libx11-data libxau6 libxaw7 libxcb1
libxdmcp6 libxext6 libxml2 libxmu6 libxpm4 libxt6 libyaml-0-2 man-db
mime-support openssl po-debconf python python-markdown python-minimal
python2.7 python2.7-minimal rake ruby ruby-did-you-mean ruby-fast-xs
ruby-hpricot ruby-minitest ruby-mustache ruby-net-telnet ruby-power-assert
ruby-rdiscount ruby-ronn ruby-test-unit ruby2.3 rubygems-integration
sbuild-build-depends-seqprep-dummy x11-common zlib1g-dev
0 upgraded, 70 newly installed, 0 to remove and 37 not upgraded.
Need to get 31.2 MB/31.2 MB of archives.
After this operation, 109 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-q6a8Wo/apt_archive ./ sbuild-build-depends-seqprep-dummy 0.invalid.0 [798 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-7 [1083 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.2-1 [88.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.9 [177 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-minimal armhf 2.7.11-4 [381 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf python2.7-minimal armhf 2.7.11-4 [1092 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf python-minimal armhf 2.7.11-1 [40.0 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf mime-support all 3.59 [36.4 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.1.1-1 [60.4 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libffi6 armhf 3.2.1-4 [18.5 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsqlite3-0 armhf 3.11.1-1 [457 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf libssl1.0.2 armhf 1.0.2g-1 [886 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libpython2.7-stdlib armhf 2.7.11-4 [1818 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf python2.7 armhf 2.7.11-4 [267 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpython-stdlib armhf 2.7.11-1 [19.5 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf python armhf 2.7.11-1 [150 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libmarkdown2 armhf 2.1.8-2 [27.7 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.3-5.2 [253 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.11.1-1 [40.9 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libyaml-0-2 armhf 0.1.6-3 [41.5 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.25-2 [250 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.25-2 [61.2 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.7-2 [111 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf libicu55 armhf 55.1-7 [7380 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.3+dfsg1-1 [800 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20150820.1 [71.7 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2g-1 [666 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.46.2-3 [2482 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-1 [131 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.7-2 [1400 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.19 [249 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.56-2 [94.9 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.016-1 [11.9 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.016-1 [6998 B]
Get:45 http://172.17.0.1/private stretch-staging/main armhf debhelper all 9.20160313 [808 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+14 [251 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf libxmu6 armhf 2:1.1.2-2 [52.0 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libxpm4 armhf 1:3.5.11-1+b1 [42.4 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libxaw7 armhf 2:1.0.13-1 [164 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf groff armhf 1.22.3-7 [3225 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf python-markdown all 2.6.6-1 [56.2 kB]
Get:55 http://172.17.0.1/private stretch-staging/main armhf rubygems-integration all 1.10 [4882 B]
Get:56 http://172.17.0.1/private stretch-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf ruby-minitest all 5.8.4-2 [50.3 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf ruby-power-assert all 0.2.7-1 [7578 B]
Get:60 http://172.17.0.1/private stretch-staging/main armhf ruby-test-unit all 3.1.7-2 [69.6 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf libruby2.3 armhf 2.3.0-5 [2834 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf ruby2.3 armhf 2.3.0-5 [167 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf ruby all 1:2.3.0+1 [10.2 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf rake all 10.5.0-2 [49.4 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf ruby-fast-xs armhf 0.8.0-3+b4 [8562 B]
Get:66 http://172.17.0.1/private stretch-staging/main armhf ruby-hpricot armhf 0.8.6-6+b1 [66.0 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf ruby-mustache all 1.0.2-1 [25.1 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf ruby-rdiscount armhf 2.1.8-1+b1 [32.9 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf ruby-ronn all 0.7.3-4 [29.6 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-seqprep-dummy.
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Unpacking sbuild-build-depends-seqprep-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Processing triggers for systemd (229-2) ...
Setting up groff-base (1.22.3-7) ...
Setting up libbsd0:armhf (0.8.2-1) ...
Setting up bsdmainutils (9.0.9) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up mime-support (3.59) ...
Setting up libexpat1:armhf (2.1.1-1) ...
Setting up libffi6:armhf (3.2.1-4) ...
Setting up libsqlite3-0:armhf (3.11.1-1) ...
Setting up libssl1.0.2:armhf (1.0.2g-1) ...
Setting up libpython2.7-stdlib:armhf (2.7.11-4) ...
Setting up python2.7 (2.7.11-4) ...
Setting up libpython-stdlib:armhf (2.7.11-1) ...
Setting up python (2.7.11-1) ...
Setting up libmarkdown2:armhf (2.1.8-2) ...
Setting up libunistring0:armhf (0.9.3-5.2) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up libxcb1:armhf (1.11.1-1) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libyaml-0-2:armhf (0.1.6-3) ...
Setting up libmagic1:armhf (1:5.25-2) ...
Setting up file (1:5.25-2) ...
Setting up gettext-base (0.19.7-2) ...
Setting up libicu55:armhf (55.1-7) ...
Setting up libxml2:armhf (2.9.3+dfsg1-1) ...
Setting up autotools-dev (20150820.1) ...
Setting up openssl (1.0.2g-1) ...
Setting up ca-certificates (20160104) ...
Setting up libglib2.0-0:armhf (2.46.2-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.11-1) ...
Setting up gettext (0.19.7-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.19) ...
Setting up libarchive-zip-perl (1.56-2) ...
Setting up libfile-stripnondeterminism-perl (0.016-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up x11-common (1:7.7+14) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxmu6:armhf (2:1.1.2-2) ...
Setting up libxpm4:armhf (1:3.5.11-1+b1) ...
Setting up libxaw7:armhf (2:1.0.13-1) ...
Setting up groff (1.22.3-7) ...
Setting up python-markdown (2.6.6-1) ...
Setting up rubygems-integration (1.10) ...
Setting up ruby-did-you-mean (1.0.0-2) ...
Setting up ruby-minitest (5.8.4-2) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up ruby-power-assert (0.2.7-1) ...
Setting up ruby-test-unit (3.1.7-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up debhelper (9.20160313) ...
Setting up rake (10.5.0-2) ...
Setting up libruby2.3:armhf (2.3.0-5) ...
Setting up ruby2.3 (2.3.0-5) ...
Setting up ruby-mustache (1.0.2-1) ...
Setting up dh-strip-nondeterminism (0.016-1) ...
Setting up ruby (1:2.3.0+1) ...
Setting up ruby-fast-xs (0.8.0-3+b4) ...
Setting up ruby-hpricot (0.8.6-6+b1) ...
Setting up ruby-rdiscount (2.1.8-1+b1) ...
Setting up ruby-ronn (0.7.3-4) ...
Setting up sbuild-build-depends-seqprep-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.22-3) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for systemd (229-2) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.26-5 dpkg-dev_1.18.4 g++-5_5.3.1-11 gcc-5_5.3.1-11 libc6-dev_2.22-3 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.114 apt_1.2.6 autotools-dev_20150820.1 base-files_9.5+rpi1 base-passwd_3.5.39 bash_4.3-14 binutils_2.26-5 bsdmainutils_9.0.9 bsdutils_1:2.27.1-6 build-essential_11.7 bzip2_1.0.6-8 ca-certificates_20160104 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:5.3.1-1+rpi1 cpp-5_5.3.1-11 dash_0.5.8-2.1 debconf_1.5.59 debfoster_2.7-2 debhelper_9.20160313 debianutils_4.7 dh-strip-nondeterminism_0.016-1 diffutils_1:3.3-3 dmsetup_2:1.02.116-1 dpkg_1.18.4 dpkg-dev_1.18.4 e2fslibs_1.42.13-1 e2fsprogs_1.42.13-1 fakeroot_1.20.2-1 file_1:5.25-2 findutils_4.6.0+git+20160126-2 g++_4:5.3.1-1+rpi1 g++-5_5.3.1-11 gcc_4:5.3.1-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-12 gcc-5_5.3.1-11 gcc-5-base_5.3.1-11 gettext_0.19.7-2 gettext-base_0.19.7-2 gnupg_1.4.20-4 gpgv_1.4.20-4 grep_2.22-1 groff_1.22.3-7 groff-base_1.22.3-7 gzip_1.6-4 hostname_3.17 init_1.29 init-system-helpers_1.29 initscripts_2.88dsf-59.3 insserv_1.14.0-5.3 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-8+rpi1 kmod_22-1 libacl1_2.2.52-3 libapparmor1_2.10-3 libapt-pkg5.0_1.2.6 libarchive-zip-perl_1.56-2 libasan2_5.3.1-11 libatomic1_5.3.1-11 libattr1_1:2.4.47-2 libaudit-common_1:2.4.5-1 libaudit1_1:2.4.5-1 libblkid1_2.27.1-6 libbsd0_0.8.2-1 libbz2-1.0_1.0.6-8 libc-bin_2.22-3 libc-dev-bin_2.22-3 libc6_2.22-3 libc6-dev_2.22-3 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-11 libcomerr2_1.42.13-1 libcroco3_0.6.11-1 libcryptsetup4_2:1.7.0-2 libdb5.3_5.3.28-11 libdbus-1-3_1.10.8-1 libdebconfclient0_0.207 libdevmapper1.02.1_2:1.02.116-1 libdpkg-perl_1.18.4 libdrm2_2.4.67-1 libexpat1_2.1.1-1 libfakeroot_1.20.2-1 libfdisk1_2.27.1-6 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.016-1 libgc1c2_1:7.4.2-7.3 libgcc-5-dev_5.3.1-11 libgcc1_1:5.3.1-11 libgcrypt20_1.6.5-2 libgdbm3_1.8.3-13.1 libglib2.0-0_2.46.2-3 libgmp10_2:6.1.0+dfsg-2 libgomp1_5.3.1-11 libgpg-error0_1.21-2 libice6_2:1.0.9-1+b1 libicu55_55.1-7 libisl15_0.16.1-1 libklibc_2.0.4-8+rpi1 libkmod2_22-1 liblz4-1_0.0~r131-2 liblzma5_5.1.1alpha+20120614-2.1 libmagic1_1:5.25-2 libmarkdown2_2.1.8-2 libmount1_2.27.1-6 libmpc3_1.0.3-1 libmpfr4_3.1.4-1 libncurses5_6.0+20160213-1 libncursesw5_6.0+20160213-1 libpam-modules_1.1.8-3.2 libpam-modules-bin_1.1.8-3.2 libpam-runtime_1.1.8-3.2 libpam0g_1.1.8-3.2 libpcre3_2:8.38-3 libperl5.22_5.22.1-9 libpipeline1_1.4.1-2 libpng12-0_1.2.54-4 libprocps5_2:3.3.11-3 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-4 libpython2.7-stdlib_2.7.11-4 libreadline6_6.3-8+b3 libruby2.3_2.3.0-5 libseccomp2_2.2.3-3 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libsm6_2:1.2.2-1+b1 libsmartcols1_2.27.1-6 libsqlite3-0_3.11.1-1 libss2_1.42.13-1 libssl1.0.2_1.0.2g-1 libstdc++-5-dev_5.3.1-11 libstdc++6_5.3.1-11 libsystemd0_229-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20160213-1 libubsan0_5.3.1-11 libudev1_229-2 libunistring0_0.9.3-5.2 libusb-0.1-4_2:0.1.12-28 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-6 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb1_1.11.1-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxml2_2.9.3+dfsg1-1 libxmu6_2:1.1.2-2 libxpm4_1:3.5.11-1+b1 libxt6_1:1.1.5-1 libyaml-0-2_0.1.6-3 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.1 lsb-base_9.20160110+rpi1 make_4.1-6 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.04-2 mawk_1.3.3-17 mime-support_3.59 mount_2.27.1-6 multiarch-support_2.22-3 nano_2.5.3-2 ncurses-base_6.0+20160213-1 ncurses-bin_6.0+20160213-1 openssl_1.0.2g-1 passwd_1:4.2-3.1 patch_2.7.5-1 perl_5.22.1-9 perl-base_5.22.1-9 perl-modules-5.22_5.22.1-9 po-debconf_1.0.19 procps_2:3.3.11-3 python_2.7.11-1 python-markdown_2.6.6-1 python-minimal_2.7.11-1 python2.7_2.7.11-4 python2.7-minimal_2.7.11-4 rake_10.5.0-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-8 ruby_1:2.3.0+1 ruby-did-you-mean_1.0.0-2 ruby-fast-xs_0.8.0-3+b4 ruby-hpricot_0.8.6-6+b1 ruby-minitest_5.8.4-2 ruby-mustache_1.0.2-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.2.7-1 ruby-rdiscount_2.1.8-1+b1 ruby-ronn_0.7.3-4 ruby-test-unit_3.1.7-2 ruby2.3_2.3.0-5 rubygems-integration_1.10 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-seqprep-dummy_0.invalid.0 sed_4.2.2-7.1 sensible-utils_0.0.9 startpar_0.59-3 systemd_229-2 systemd-sysv_229-2 sysv-rc_2.88dsf-59.3 sysvinit-utils_2.88dsf-59.3 tar_1.28-2.1 tzdata_2016a-1 udev_229-2 util-linux_2.27.1-6 x11-common_1:7.7+14 xz-utils_5.1.1alpha+20120614-2.1 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Mar 21 20:26:48 2016 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./seqprep_1.1-6.dsc
dpkg-source: info: extracting seqprep in seqprep-1.1
dpkg-source: info: unpacking seqprep_1.1.orig.tar.gz
dpkg-source: info: unpacking seqprep_1.1-6.debian.tar.xz
dpkg-source: info: applying fix_unused_variable_errors.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying replace-float-with-double.patch
Check disc 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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-1a6e1942-40ed-43af-9ece-31059339542d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: source package seqprep
dpkg-buildpackage: source version 1.1-6
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build seqprep-1.1
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm SeqPrep.o utils.o stdaln.o SeqPrep
rm: cannot remove 'SeqPrep.o': No such file or directory
rm: cannot remove 'utils.o': No such file or directory
rm: cannot remove 'stdaln.o': No such file or directory
rm: cannot remove 'SeqPrep': No such file or directory
Makefile:22: recipe for target 'clean' failed
make[1]: [clean] Error 1 (ignored)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_clean
rm -f seqprep
rm -f debian/*.1
rm -f README.html
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_testdir -a
dh_update_autotools_config -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -Werror -O0 -g SeqPrep.c -o SeqPrep.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -Werror -O0 -g utils.c -o utils.o
gcc -g -O2 -fPIE -fstack-protector-strong -Wformat -Werror=format-security -std=gnu90 -c -Wall -Werror -O0 -g stdaln.c -o stdaln.o
gcc SeqPrep.o utils.o stdaln.o -fPIE -pie -Wl,-z,relro -Wl,-z,now -lz -lm -o SeqPrep
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
cp SeqPrep seqprep
TZ=UTC ronn -r --manual=seqprep --organization='Cancer Therapeutics Innovation Group' debian/seqprep.1.ronn
roff: debian/seqprep.1
markdown_py -f README.html README.md
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# This checks that the tests run and produce byte-identical results.
cd Test && mkdir -p out info && \
bash -xc 'gzcat(){ zcat "$@" ; } ; . RUNTEST.sh'
+ . RUNTEST.sh
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_merged_1.fastq.gz -2 ./out/pe_bad_contam_merged_2.fastq.gz -s ./out/pe_bad_contam_merged_s.fastq.gz -E ./info/alignments_merged.txt.gz
Processing reads... |/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\fastq record not beginning with @
fastq record not beginning with @
Pairs Processed: 100000
Pairs Merged: 14314
Pairs With Adapters: 4091
Pairs Discarded: 2228
CPU Time Used (Minutes): 2.070528
++ ../SeqPrep -6 -f ./data/multiplex_bad_contam_1.fq.gz -r ./data/multiplex_bad_contam_2.fq.gz -A GATCGGAAGAGCACACGTCT -B AGATCGGAAGAGCGTCGT -1 ./out/pe_bad_contam_trimmed_1.fastq.gz -2 ./out/pe_bad_contam_trimmed_2.fastq.gz -E ./info/alignments_trimmed.txt.gz
Processing reads... |/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\|/-\fastq record not beginning with @
fastq record not beginning with @
Pairs Processed: 100000
Pairs Merged: 0
Pairs With Adapters: 4091
Pairs Discarded: 2228
CPU Time Used (Minutes): 1.992044
++ prog=gzcat
++ python seqlens.py
++ gzcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ zcat ./out/pe_bad_contam_trimmed_1.fastq.gz
++ gzcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ zcat ./out/pe_bad_contam_trimmed_2.fastq.gz
++ python seqlens.py
++ gzcat ./out/pe_bad_contam_merged_1.fastq.gz
++ zcat ./out/pe_bad_contam_merged_1.fastq.gz
++ python seqlens.py
++ gzcat ./out/pe_bad_contam_merged_2.fastq.gz
++ zcat ./out/pe_bad_contam_merged_2.fastq.gz
++ python seqlens.py
++ gzcat ./out/pe_bad_contam_merged_s.fastq.gz
++ zcat ./out/pe_bad_contam_merged_s.fastq.gz
++ python seqlens.py
[ `cat Test/info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ]
# remove output dirs right after testing to make sure the files
# will not be included in the data package
rm -rf Test/info Test/out
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j1 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp SeqPrep /sbuild-nonexistent/bin
cp: cannot create regular file '/sbuild-nonexistent/bin': No such file or directory
Makefile:16: recipe for target 'install' failed
make[1]: [install] Error 1 (ignored)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'seqprep-dbgsym' in '../seqprep-dbgsym_1.1-6_armhf.deb'.
dpkg-deb: building package 'seqprep' in '../seqprep_1.1-6_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../seqprep_1.1-6_armhf.changes
dpkg-genchanges: warning: package seqprep-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build seqprep-1.1
dpkg-buildpackage: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 20160329-1125
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
seqprep_1.1-6_armhf.changes:
----------------------------
Format: 1.8
Date: Mon, 21 Mar 2016 21:24:52 +0100
Source: seqprep
Binary: seqprep seqprep-data
Architecture: armhf
Version: 1.1-6
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
seqprep - stripping adaptors and/or merging paired reads of DNA sequences w
seqprep-data - example data set for seqprep - only used for testing
Closes: 818918
Changes:
seqprep (1.1-6) unstable; urgency=medium
.
* Add missing Python dependency to tests (Thanks for the patch to
Steve Langasek <steve.langasek@canonical.com>)
Closes: #818918
Checksums-Sha1:
c9273d88a5ccae39b139b1413d97a75fc816561b 15340 seqprep-dbgsym_1.1-6_armhf.deb
a25599323c6655faf8836e7c9ae4ab034af24afe 26566 seqprep_1.1-6_armhf.deb
Checksums-Sha256:
d4103557f985f5c738f1123b3893f862d43741ec4ddd885890d2d3500fc6ebbc 15340 seqprep-dbgsym_1.1-6_armhf.deb
646afeb548a1ce366fe782cef0a0a042477d756dc2d581c59f71f6e86e2dccc3 26566 seqprep_1.1-6_armhf.deb
Files:
70002e11838fa2e9cc7413a58698e949 15340 debug extra seqprep-dbgsym_1.1-6_armhf.deb
11fc9b2d0c84f9aed1e5e9f9de61a1bb 26566 science optional seqprep_1.1-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
seqprep-dbgsym_1.1-6_armhf.deb
------------------------------
new debian package, version 2.0.
size 15340 bytes: control archive=491 bytes.
407 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: seqprep-dbgsym
Source: seqprep
Version: 1.1-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 31
Depends: seqprep (= 1.1-6)
Section: debug
Priority: extra
Homepage: http://seqanswers.com/wiki/SeqPrep
Description: Debug symbols for seqprep
Auto-Built-Package: debug-symbols
Build-Ids: e973fda20da706a64da9aba21cf434f9524298a5
drwxr-xr-x root/root 0 2016-03-29 11:25 ./
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/lib/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/lib/debug/.build-id/e9/
-rw-r--r-- root/root 20632 2016-03-29 11:25 ./usr/lib/debug/.build-id/e9/73fda20da706a64da9aba21cf434f9524298a5.debug
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/share/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-03-29 11:25 ./usr/share/doc/seqprep-dbgsym -> seqprep
seqprep_1.1-6_armhf.deb
-----------------------
new debian package, version 2.0.
size 26566 bytes: control archive=1021 bytes.
1170 bytes, 21 lines control
326 bytes, 5 lines md5sums
Package: seqprep
Version: 1.1-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 118
Depends: libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: science
Priority: optional
Homepage: http://seqanswers.com/wiki/SeqPrep
Description: stripping adaptors and/or merging paired reads of DNA sequences with overlap
SeqPrep is a program to merge paired end Illumina reads that are overlapping
into a single longer read. It may also just be used for its adapter trimming
feature without doing any paired end overlap. When an adapter sequence is
present, that means that the two reads must overlap (in most cases) so they
are forcefully merged. When reads do not have adapter sequence they must be
treated with care when doing the merging, so a much more specific approach is
taken. The default parameters were chosen with specificity in mind, so that
they could be ran on libraries where very few reads are expected to overlap.
It is always safest though to save the overlapping procedure for libraries
where you have some prior knowledge that a significant portion of the reads
will have some overlap.
drwxr-xr-x root/root 0 2016-03-29 11:25 ./
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/
drwxr-xr-x root/root 0 2016-03-29 11:25 ./usr/bin/
-rwxr-xr-x root/root 90600 2016-03-29 11:25 ./usr/bin/seqprep
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/share/
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/share/doc/seqprep/
-rw-r--r-- root/root 11704 2016-03-29 11:20 ./usr/share/doc/seqprep/README.html
-rw-r--r-- root/root 766 2016-03-21 20:24 ./usr/share/doc/seqprep/changelog.Debian.gz
-rw-r--r-- root/root 1375 2015-02-20 13:25 ./usr/share/doc/seqprep/copyright
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/share/man/
drwxr-xr-x root/root 0 2016-03-29 11:24 ./usr/share/man/man1/
-rw-r--r-- root/root 4568 2016-03-29 11:24 ./usr/share/man/man1/seqprep.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 65004
Build-Time: 286
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 386
Job: seqprep_1.1-6
Machine Architecture: armhf
Package: seqprep
Package-Time: 731
Source-Version: 1.1-6
Space: 65004
Status: successful
Version: 1.1-6
--------------------------------------------------------------------------------
Finished at 20160329-1125
Build needed 00:12:11, 65004k disc space