[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_1 #4490
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Dec 19 23:01:57 UTC 2015
See <https://jenkins.debian.net/job/reproducible_builder_armhf_1/4490/>
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[...truncated 632 lines...]
dpkg-buildpackage: architecture hôte armhf
fakeroot debian/rules clean
dh clean
dh_testdir
dh_auto_clean
make -j1 clean
make[1]: Entering directory '/build/perm-0.4.0'
rm -f *.o *.exe cut out perm perm.tar.gz
make[1]: Leaving directory '/build/perm-0.4.0'
dh_clean
debian/rules build
dh build
dh_testdir
dh_auto_configure
dh_auto_build
make -j1
make[1]: Entering directory '/build/perm-0.4.0'
make clean
make[2]: Entering directory '/build/perm-0.4.0'
rm -f *.o *.exe cut out perm perm.tar.gz
make[2]: Leaving directory '/build/perm-0.4.0'
g++ -O2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -o perm -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp AlignmentsQ.cpp Filename.cpp GenomeNTdata.cpp ReadInBits.cpp PerM.cpp chromosomeNTdata.cpp bitsOperationUtil.cpp FileOutputBuffer.cpp HashIndexT.cpp ReadInBitsSet.cpp SeedPattern.cpp boolFlagArray.cpp GenomeInBits.cpp Index_Table.cpp ReadsMapping.cpp PairedReadsMapping.cpp ShortReadUtil.cpp chdir.cpp Genome_Index.cpp MismatchScores.cpp stdafx.cpp Flags.cpp ParseReadsOpts.cpp ColorSpaceRead.cpp Genome_Index_Table.cpp ParameterList.cpp ReadsMappingStats.cpp FileInputBuffer.cpp Genome_Index_TableQ.cpp ReadsQualScores.cpp ChrIndex2GeneName.cpp ReadsFileParser.cpp PairedReadsSet.cpp MappingResult.cpp refInBinFile.cpp LongReadsSet.cpp -lm -lstdc++ -Wl,-z,relro
In file included from ReadsMappingStats.h:3:0,
from ReadsMapping.h:10,
from PairedReadsMapping.h:2,
from PerM.cpp:8:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from GenomeInBits.h:9:0,
from GenomeInBits.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from ReadsMappingStats.h:3:0,
from ReadsMapping.h:10,
from ReadsMapping.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from ReadsMappingStats.h:3:0,
from ReadsMapping.h:10,
from PairedReadsMapping.h:2,
from PairedReadsMapping.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from Genome_Index.h:8:0,
from Genome_Index.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from GenomeInBits.h:9:0,
from refInBinFile.h:3,
from Genome_Index_Table.h:8,
from Genome_Index_Table.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
ParameterList.cpp: In member function ‘void MappingOpts::setDefaults()’:
ParameterList.cpp:31:9: warning: unused variable ‘mismatchScoreThreshold’ [-Wunused-variable]
int mismatchScoreThreshold = -1; // No filtering by sum of mismatch score
^
In file included from ReadsMappingStats.h:3:0,
from ReadsMappingStats.cpp:2:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
Genome_Index_TableQ.cpp: In member function ‘unsigned int CGenome_Index_TableQ::extendAlignment(CAlignmentsQ&, CReadInBits) const’:
Genome_Index_TableQ.cpp:364:10: warning: variable ‘extendForward’ set but not used [-Wunused-but-set-variable]
bool extendForward = true;
^
In file included from GenomeInBits.h:9:0,
from refInBinFile.h:3,
from Genome_Index_Table.h:8,
from Genome_Index_TableQ.h:2,
from Genome_Index_TableQ.cpp:1:
GenomeNTdata.h: At global scope:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
In file included from GenomeInBits.h:9:0,
from refInBinFile.h:3,
from refInBinFile.cpp:1:
GenomeNTdata.h:12:20: warning: ‘BAD_GENOME_INDEX’ defined but not used [-Wunused-variable]
const unsigned int BAD_GENOME_INDEX = std::numeric_limits<unsigned int>::max();
^
#g++ -O2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -o perm *.o -lm -lstdc++
make[1]: Leaving directory '/build/perm-0.4.0'
dh_auto_test
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/perm-0.4.0'
#
make[1]: Leaving directory '/build/perm-0.4.0'
dh_install
dh_installdocs
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: avertissement: debian/perm/usr/bin/perm contient une référence au symbole __aeabi_atexit at CXXABI_ARM_1.3.3 qui ne peut être résolue : il peut s'agir d'un greffon (« plugin »)
dpkg-shlibdeps: avertissement: la dépendance pourrait être évitée si « debian/perm/usr/bin/perm » n'y était pas lié avec ld-linux-armhf.so.3 sans nécessité (il n'utilise aucun des symboles de la bibliothèque)
dh_installdeb
dh_gencontrol
dpkg-gencontrol: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
dpkg-gencontrol: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
dh_md5sums
dh_builddeb
dpkg-deb : construction du paquet « perm-dbgsym » dans « ../perm-dbgsym_0.4.0-1_armhf.deb ».
dpkg-deb : construction du paquet « perm » dans « ../perm_0.4.0-1_armhf.deb ».
dpkg-genbuildinfo >../perm_0.4.0-1_armhf.buildinfo
dpkg-distaddfile perm_0.4.0-1_armhf.buildinfo science optional
dpkg-distaddfile: avertissement: Fichier::FcntlLock non disponible; utilisation de « flock » qui n'est pas sécurisé pour NFS
dpkg-genchanges -b >../perm_0.4.0-1_armhf.changes
dpkg-genchanges: avertissement: paquet perm-dbgsym listé dans le fichier de liste des fichiers mais pas dans le fichier info
dpkg-genchanges: envoi des binaires seulement (le code source n'est pas inclus)
dpkg-source --after-build perm-0.4.0
dpkg-buildpackage: envoi d'un binaire seulement (aucune inclusion de code source)
I: user script /srv/workspace/pbuilder/6372/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/6372/tmp/hooks/B01_cleanup finished
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
I: unmounting /sys filesystem
/usr/lib/pbuilder/pbuilder-modules: line 164: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
I: unmounting /dev/shm filesystem
/usr/lib/pbuilder/pbuilder-modules: line 164: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
I: unmounting dev/pts filesystem
/usr/lib/pbuilder/pbuilder-modules: line 164: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
I: unmounting run/shm filesystem
/usr/lib/pbuilder/pbuilder-modules: line 164: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
LANGUAGE = (unset),
LC_ALL = "fr_CH.UTF-8",
LANG = "fr_CH.UTF-8"
are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
I: unmounting proc filesystem
/usr/lib/pbuilder/pbuilder-modules: line 164: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8)
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/6372 and its subdirectories
I: Current time: Sun Dec 20 13:01:48 GMT-14 2015
I: pbuilder-time-stamp: 1450566108
+ PRESULT=0
+ set -e
+ '[' 0 -eq 124 ']'
+ false
+ set +x
Sat Dec 19 23:01:48 UTC 2015 - build #2 for perm/unstable/armhf on odxu4 done.
/srv/reproducible-results/rbuild-debian-EFWfZKMU/tmp.mN5QTRwbXE: 46.5% -- replaced with /srv/reproducible-results/rbuild-debian-EFWfZKMU/tmp.mN5QTRwbXE.gz
Sat Dec 19 23:01:48 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-0V4ovdTw, which will now be removed.
/srv/reproducible-results/rbuild-debian-g3roQ3j0:
total 36
drwxr-xr-x 2 jenkins jenkins 4096 Dec 19 22:57 b1
drwxr-xr-x 2 jenkins jenkins 4096 Dec 19 23:01 b2
-rw-r--r-- 1 jenkins jenkins 1962 Apr 25 2014 perm_0.4.0-1.dsc
-rw------- 1 jenkins jenkins 20968 Dec 19 22:58 tmp.uAzG2MlDlc
/srv/reproducible-results/rbuild-debian-g3roQ3j0/b1:
total 268
-rw-r--r-- 1 jenkins jenkins 18321 Dec 19 22:57 build.log
-rw-r--r-- 1 jenkins jenkins 8980 Dec 19 22:57 perm_0.4.0-1.debian.tar.xz
-rw-r--r-- 1 jenkins jenkins 1962 Dec 19 22:57 perm_0.4.0-1.dsc
-rw-r--r-- 1 jenkins jenkins 775 Dec 19 22:57 perm_0.4.0-1_armhf.changes
-rw-r--r-- 1 jenkins jenkins 110488 Dec 19 22:57 perm_0.4.0-1_armhf.deb
-rw-r--r-- 1 jenkins jenkins 114025 Dec 19 22:57 perm_0.4.0.orig.tar.gz
/srv/reproducible-results/rbuild-debian-g3roQ3j0/b2:
total 1084
-rw-r--r-- 1 jenkins jenkins 14467 Dec 19 23:01 build.log
-rw-r--r-- 1 jenkins jenkins 823128 Dec 19 23:01 perm-dbgsym_0.4.0-1_armhf.deb
-rw-r--r-- 1 jenkins jenkins 8980 Dec 19 23:01 perm_0.4.0-1.debian.tar.xz
-rw-r--r-- 1 jenkins jenkins 1962 Dec 19 23:01 perm_0.4.0-1.dsc
-rw-r--r-- 1 jenkins jenkins 4391 Dec 19 23:01 perm_0.4.0-1_armhf.buildinfo
-rw-r--r-- 1 jenkins jenkins 1301 Dec 19 23:01 perm_0.4.0-1_armhf.changes
-rw-r--r-- 1 jenkins jenkins 110602 Dec 19 23:01 perm_0.4.0-1_armhf.deb
-rw-r--r-- 1 jenkins jenkins 114025 Dec 19 23:01 perm_0.4.0.orig.tar.gz
Format: 1.8
Date: Fri, 25 Apr 2014 18:39:38 +0200
Source: perm
Binary: perm
Architecture: armhf
Version: 0.4.0-1
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:
perm - efficient mapping of short reads with periodic spaced seeds
Closes: 745847
Changes:
perm (0.4.0-1) unstable; urgency=medium
.
* Initial upload to Debian (Closes: #745847)
Checksums-Sha1:
1514ecc957e609c39a8cc925043d2867989afa2a 110488 perm_0.4.0-1_armhf.deb
Checksums-Sha256:
3e9fd9a488ac014a1b69c2e5e2a609866340a38e084c9fa84c91f76bc216eb6f 110488 perm_0.4.0-1_armhf.deb
Files:
8d5760fe13dd54578b0f5249c931ee8d 110488 science optional perm_0.4.0-1_armhf.deb
grep-dctrl: ./b1/perm_0.4.0-1_armhf.buildinfo: No such file or directory
/srv/reproducible-results/rbuild-debian-g3roQ3j0/tmp.uAzG2MlDlc: 71.5% -- replaced with /srv/reproducible-results/rbuild-debian-g3roQ3j0/tmp.uAzG2MlDlc.gz
INFO: Starting at 2015-12-19 23:01:57.358742
INFO: Finished at 2015-12-19 23:01:57.380245, took: 0:00:00.021515
Sat 19 Dec 23:01:57 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-D1Wjp6JF, which will now be removed.
Build step 'Execute shell' marked build as failure
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