[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_12 #53547
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Oct 15 01:25:51 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_12/53547/------------------------------------------
[...truncated 7172 lines...]
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 4.4
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 4.6
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 5.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 6.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 7.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 7.2
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 7.3
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 8.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 9.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 10.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 11.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 11.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 12.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 12.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 12.2
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 13.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 13.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
running 14.0
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
++++++++++++++++++++++++++++++++++++++++++++++++++++++
Run /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/test-bin/wb-test-fastq
Running 99 test cases...
*** No errors detected
++++++++++++++++++++++++++++++++++++++++++++++++++++++
Run /build/sra-sdk-2.7.0/debian/tmp/usr/sra-tools/linux/gcc/x86_64/rel/test-bin/test-fastq-loader
Running 1 test case...
*** No errors detected
make[3] : on quitte le répertoire « /build/sra-sdk-2.7.0/test/fastq-loader »
make[2] : on quitte le répertoire « /build/sra-sdk-2.7.0/test »
make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_testroot
debian/rules override_dh_prep
make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
dh_prep -X debian/tmp
make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_auto_install
make -j1 install DESTDIR=/build/sra-sdk-2.7.0/debian/sra-toolkit AM_UPDATE_INFO_DIR=no
make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
Checking make status of tools...
NOTE - copycat cannot be built: It requires our internal library 'libkff' which requires 'libmagic' and its development headers.
NOTE - fastq-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - illumina-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - srf-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - abi-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - sff-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - helicos-load cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - pacbio-loadxml cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - ccextract cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
NOTE - pacbio-load cannot be built: It requires our internal library 'libkdf5' which requires 'libhdf5' and its development headers.
NOTE - remote-fuser cannot be built: It requires our internal library 'libkxml' which requires 'libxml2' and its development headers.
make[2] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
Installing executables to /build/sra-sdk-2.7.0/debian/tmp/usr/bin/...
Installing abi-dump...done
Installing abi-load...not found
Installing align-info...done
Installing bam-load...done
Installing cache-mgr...done
Installing cg-load...done
Installing copycat...not found
Installing fastdump...done
Installing fastq-dump...done
Installing fastq-load...not found
Installing helicos-load...not found
Installing illumina-dump...done
Installing illumina-load...not found
Installing kar...done
Installing kdbmeta...done
Installing latf-load...done
Installing prefetch...done
Installing rcexplain...done
Installing remote-fuser...not found
Installing sam-dump...done
Installing sff-dump...done
Installing sff-load...not found
Installing srapath...done
Installing sra-pileup...done
Installing sra-sort...done
Installing sra-stat...done
Installing srf-load...not found
Installing test-sra...done
Installing vdb-config...done
Installing vdb-copy...done
Installing vdb-decrypt...done
Installing vdb-dump...done
Installing vdb-encrypt...done
Installing vdb-lock...done
Installing vdb-passwd...done
Installing vdb-unlock...done
Installing vdb-validate...done
Installing magic file...done
Installing configuration files to /etc/ncbi/...mkdir: impossible de créer le répertoire « /etc/ncbi »: Permission non accordée
done
Updating /etc/profile.d/sra-tools.[c]sh
/bin/sh: ligne 4: /etc/profile.d/sra-tools.sh: Permission non accordée
/bin/sh: ligne 4: /etc/profile.d/sra-tools.csh: Permission non accordée
make[2] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
debian/rules override_dh_install
make[1] : on entre dans le répertoire « /build/sra-sdk-2.7.0 »
# upstream installs versioned *.a libs - we only want a single version
for bin in debian/tmp/usr/bin/*[a-z] ; do \
mv debian/tmp/usr/bin/`readlink $bin` $bin ; \
mv debian/tmp/usr/bin/`readlink $bin` $bin ; \
done
mv: impossible d'écraser le non répertoire 'debian/tmp/usr/bin/magic' par le répertoire 'debian/tmp/usr/bin/'
mv: impossible d'écraser le non répertoire 'debian/tmp/usr/bin/magic' par le répertoire 'debian/tmp/usr/bin/'
dh_install
# remove susipcious file which is not executable and conflicts with package magic
rm -f debian/*/usr/bin/magic
make[1] : on quitte le répertoire « /build/sra-sdk-2.7.0 »
dh_installdocs
dh_installchangelogs
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libsz.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libdl.so.2 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/sra-toolkit/usr/bin/latf-load debian/sra-toolkit/usr/bin/rcexplain debian/sra-toolkit/usr/bin/sra-stat debian/sra-toolkit/usr/bin/srapath debian/sra-toolkit/usr/bin/vdb-copy debian/sra-toolkit/usr/bin/bam-load debian/sra-toolkit/usr/bin/vdb-config debian/sra-toolkit/usr/bin/illumina-dump debian/sra-toolkit/usr/bin/sam-dump debian/sra-toolkit/usr/bin/vdb-dump debian/sra-toolkit/usr/bin/kar debian/sra-toolkit/usr/bin/align-info debian/sra-toolkit/usr/bin/cache-mgr debian/sra-toolkit/usr/bin/test-sra debian/sra-toolkit/usr/bin/vdb-validate debian/sra-toolkit/usr/bin/fastdump debian/sra-toolkit/usr/bin/vdb-decrypt debian/sra-toolkit/usr/bin/vdb-lock debian/sra-toolkit/usr/bin/fastq-dump debian/sra-toolkit/usr/bin/cg-load debian/sra-toolkit/usr/bin/sra-sort debian/sra-toolkit/usr/bin/kdbmeta debian/sra-toolkit/usr/bin/sra-pileup debian/sra-toolkit/usr/bin/vdb-encrypt debian/sra-toolkit/usr/bin/sff-dump debian/sra-toolkit/usr/bin/abi-dump debian/sra-toolkit/usr/bin/vdb-passwd debian/sra-toolkit/usr/bin/prefetch debian/sra-toolkit/usr/bin/vdb-unlock were not linked against libbz2.so.1.0 (they use none of the library's symbols)
dh_installdeb
dh_gencontrol
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
dh_builddeb
dpkg-deb: building package 'sra-toolkit-dbgsym' in '../sra-toolkit-dbgsym_2.7.0-1_amd64.deb'.
dpkg-deb: building package 'sra-toolkit' in '../sra-toolkit_2.7.0-1_amd64.deb'.
dpkg-genbuildinfo --build=any,all --buildinfo-id=amd64
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=any,all >../sra-sdk_2.7.0-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build sra-sdk-2.7.0
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
I: user script /srv/workspace/pbuilder/16784/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/16784/tmp/hooks/B01_cleanup finished
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/16784 and its subdirectories
I: Current time: samedi 15 octobre 2016, 15:25:49 (UTC+1400)
I: pbuilder-time-stamp: 1476494749
+ PRESULT=0
+ set -e
+ '[' 0 -eq 124 ']'
+ false
+ set +x
Sat Oct 15 01:25:49 UTC 2016 - build #2 for sra-sdk/testing/amd64 on profitbricks-build1-amd64 done.
/srv/reproducible-results/rbuild-debian-40ChHcNZ/tmp.wi6RgmUG9D: 49.8% -- replaced with /srv/reproducible-results/rbuild-debian-40ChHcNZ/tmp.wi6RgmUG9D.gz
Sat Oct 15 01:25:49 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-U01hDWqf, which will now be removed.
/srv/reproducible-results/rbuild-debian-mOO7KO1e:
total 420
drwxr-xr-x 2 jenkins jenkins 4096 Oct 15 01:20 b1
drwxr-xr-x 2 jenkins jenkins 4096 Oct 15 01:25 b2
-rw-r--r-- 1 jenkins jenkins 2012 Sep 1 14:02 sra-sdk_2.7.0-1.dsc
-rw------- 1 jenkins jenkins 411988 Oct 15 01:20 tmp.Ip72KQlPGf
/srv/reproducible-results/rbuild-debian-mOO7KO1e/b1:
total 3628
-rw-r--r-- 1 jenkins jenkins 408807 Oct 15 01:20 build.log
-rw-r--r-- 1 jenkins jenkins 4827 Oct 15 01:20 sra-sdk_2.7.0-1_amd64.buildinfo
-rw-r--r-- 1 jenkins jenkins 1756 Oct 15 01:20 sra-sdk_2.7.0-1_amd64.changes
-rw-r--r-- 1 jenkins jenkins 2100964 Oct 15 01:20 sra-toolkit-dbgsym_2.7.0-1_amd64.deb
-rw-r--r-- 1 jenkins jenkins 1177508 Oct 15 01:20 sra-toolkit_2.7.0-1_amd64.deb
/srv/reproducible-results/rbuild-debian-mOO7KO1e/b2:
total 3640
-rw-r--r-- 1 jenkins jenkins 418311 Oct 15 01:25 build.log
-rw-r--r-- 1 jenkins jenkins 4827 Oct 15 01:25 sra-sdk_2.7.0-1_amd64.buildinfo
-rw-r--r-- 1 jenkins jenkins 1756 Oct 15 01:25 sra-sdk_2.7.0-1_amd64.changes
-rw-r--r-- 1 jenkins jenkins 2100964 Oct 15 01:25 sra-toolkit-dbgsym_2.7.0-1_amd64.deb
-rw-r--r-- 1 jenkins jenkins 1177508 Oct 15 01:25 sra-toolkit_2.7.0-1_amd64.deb
Sat Oct 15 01:25:50 UTC 2016 I: sra-sdk_2.7.0-1_amd64.changes:
Format: 1.8
Date: Thu, 01 Sep 2016 15:41:02 +0200
Source: sra-sdk
Binary: sra-toolkit
Architecture: amd64
Version: 2.7.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Andreas Tille <tille at debian.org>
Description:
sra-toolkit - utilities for the NCBI Sequence Read Archive
Closes: 680436 769050
Changes:
sra-sdk (2.7.0-1) unstable; urgency=medium
.
[ Andreas Tille ]
* New upstream version
Closes: #680436, #769050
* d/watch points to github
* d/copyright: no need to exclude any files any more
* cme fix dpkg-control
* New Build-Depends: libhdf5-dev, libngs-sdk-dev (>= 1.2.4)
* drop library packages since these are now build by ncbi-vdb
* use Github as homepage
.
[ Steffen Moeller and Jon Ison ]
* Introduced EDAM annotation to debian/upstream/edam
Checksums-Sha1:
f19bf48a538867e441c4d16ce431b17c971b3386 4827 sra-sdk_2.7.0-1_amd64.buildinfo
af7f0a0a46429e7fb39cbf1cd510d922af52d1f9 2100964 sra-toolkit-dbgsym_2.7.0-1_amd64.deb
c62f64debb6014f15a1cd67ad41d44a4a7fa83f6 1177508 sra-toolkit_2.7.0-1_amd64.deb
Checksums-Sha256:
1f9180c979603e5836eab68911cfecfb85a105747d1148f966534a87c13a12ce 4827 sra-sdk_2.7.0-1_amd64.buildinfo
d50174fa1288317baf373df320b50ed4bd30d109c013166ab3465456d49b1c33 2100964 sra-toolkit-dbgsym_2.7.0-1_amd64.deb
fdb4b0c87269e390baa1fd66118867b3f839cd1738ff062860822528f197e1ed 1177508 sra-toolkit_2.7.0-1_amd64.deb
Files:
68dc5f99a4f5a3ec36afbf1423d0501e 4827 science optional sra-sdk_2.7.0-1_amd64.buildinfo
17c28be607b103b27ba33fb503d49ce2 2100964 debug extra sra-toolkit-dbgsym_2.7.0-1_amd64.deb
99252b63a3e148bd022507c859ad9cc9 1177508 science optional sra-toolkit_2.7.0-1_amd64.deb
Diff of the two buildlogs:
--
tee: /var/lib/jenkins/userContent/reproducible/debian/logdiffs/testing/amd64/sra-sdk_2.7.0-1.diff: No space left on device
/srv/reproducible-results/rbuild-debian-mOO7KO1e/tmp.Ip72KQlPGf: 93.3% -- replaced with /srv/reproducible-results/rbuild-debian-mOO7KO1e/tmp.Ip72KQlPGf.gz
INFO: Starting at 2016-10-15 01:25:51.491579
INFO: Finished at 2016-10-15 01:25:51.601384, took: 0:00:00.109816
Sat 15 Oct 01:25:51 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-VJpQwbqz, which will now be removed.
Build step 'Execute shell' marked build as failure
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