[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_5 #1368
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Sep 5 22:52:06 UTC 2015
See <https://jenkins.debian.net/job/reproducible_builder_amd64_5/1368/>
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[...truncated 806 lines...]
checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... yes
checking for /usr/lib... yes
checking for readline in -lreadline... yes
checking for rl_completion_matches function... yes
checking for 32 or 64 bits cpu... 64
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
make[1]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
# build mb-mpi (from initial config)
LIBS="-Wl,--as-needed" dh_auto_build
make -j1
make[2]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c
mpicc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm
make[2]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
mv src/mb ./mb-mpi
# Now - build mb
( cd src ; make clean )
make[2]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
rm -f *.o *~ mb
make[2]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
dh_auto_configure -- --with-beagle=/usr --enable-mpi=no --enable-debug=yes
./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --libexecdir=\${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --with-beagle=/usr --enable-mpi=no --enable-debug=yes
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
configure: NOTICE: Because the variable $CFLAGS is defined in your shell, the
default MrBayes flags will be overridden. To ensure optimal performance, please check
that your $CFLAGS variable is set correctly. Alternatively, unset the $CFLAGS
variable in your shell in order to use the default MrBayes compiler options.
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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for exp in -lm... yes
checking for a BSD-compatible install... /usr/bin/install -c
checking for SSE support... yes
checking for /usr/include/libhmsbeagle/libhmsbeagle/beagle.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/beagle.h... yes
checking for /usr/include/libhmsbeagle/libhmsbeagle/platform.h... no
checking for /usr/include/libhmsbeagle-1/libhmsbeagle/platform.h... yes
checking for /usr/lib... yes
checking for readline in -lreadline... yes
checking for rl_completion_matches function... yes
checking for 32 or 64 bits cpu... 64
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
LIBS="-Wl,--as-needed" dh_auto_build
make -j1
make[2]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o bayes.o bayes.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o command.o command.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o model.o model.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mcmc.o mcmc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o likelihood.o likelihood.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o proposal.o proposal.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o sumpt.o sumpt.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o utils.o utils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o mbbeagle.o mbbeagle.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -Wdate-time -D_FORTIFY_SOURCE=2 -c -o best.o best.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/libhmsbeagle-1 -DUSECONFIG_H -o mb bayes.o command.o model.o mcmc.o likelihood.o proposal.o sumpt.o utils.o mbbeagle.o best.o -Wl,-z,relro -L/usr/lib -lhmsbeagle -lreadline -lm
make[2]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg/src'
mv src/mb .
make[1]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_auto_test -O--sourcedirectory=src
fakeroot debian/rules binary
dh binary --sourcedirectory=src
dh_testroot -O--sourcedirectory=src
dh_prep -O--sourcedirectory=src
debian/rules override_dh_auto_install
make[1]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
echo "Do not try to install to /usr/local/bin"
Do not try to install to /usr/local/bin
make[1]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_install -O--sourcedirectory=src
dh_installdocs -O--sourcedirectory=src
dh_installchangelogs -O--sourcedirectory=src
dh_installman -O--sourcedirectory=src
dh_perl -O--sourcedirectory=src
dh_link -O--sourcedirectory=src
dh_strip_nondeterminism -O--sourcedirectory=src
debian/rules override_dh_compress
make[1]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_compress --exclude=.pdf
make[1]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_fixperms -O--sourcedirectory=src
debian/rules override_dh_strip
make[1]: Entering directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_strip --dbg-package=mrbayes-dbg
make[1]: Leaving directory '/tmp/buildd/mrbayes-3.2.5+dfsg'
dh_makeshlibs -O--sourcedirectory=src
dh_shlibdeps -O--sourcedirectory=src
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against libhwloc.so.5 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against libdl.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/mrbayes-mpi/usr/lib/mrbayes-mpi/mb-mpi was not linked against libpthread.so.0 (it uses none of the library's symbols)
dh_installdeb -O--sourcedirectory=src
dh_gencontrol -O--sourcedirectory=src
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
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 -O--sourcedirectory=src
dh_builddeb -O--sourcedirectory=src
dpkg-deb: building package 'mrbayes' in '../mrbayes_3.2.5+dfsg-2_amd64.deb'.
dpkg-deb: building package 'mrbayes-doc' in '../mrbayes-doc_3.2.5+dfsg-2_all.deb'.
dpkg-deb: building package 'mrbayes-dbg' in '../mrbayes-dbg_3.2.5+dfsg-2_amd64.deb'.
dpkg-deb: building package 'mrbayes-mpi' in '../mrbayes-mpi_3.2.5+dfsg-2_amd64.deb'.
dpkg-genbuildinfo >../mrbayes_3.2.5+dfsg-2_amd64.buildinfo
dpkg-distaddfile mrbayes_3.2.5+dfsg-2_amd64.buildinfo science optional
dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges -b >../mrbayes_3.2.5+dfsg-2_amd64.changes
dpkg-genchanges: binary-only upload (no source code included)
dpkg-source --after-build mrbayes-3.2.5+dfsg
dpkg-buildpackage: binary-only upload (no source included)
I: unmounting /sys filesystem
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: cleaning the build env
I: removing directory /var/cache/pbuilder/build//28177 and its subdirectories
I: Current time: Sat Sep 5 10:54:42 GMT+12 2015
I: pbuilder-time-stamp: 1441493682
+ true
+ rm /srv/reproducible-results/tmp.aRmAOjkTW3/pbuilderrc_L4DL
++ date -u
Sat Sep 5 22:54:42 UTC 2015 - build #1 for mrbayes/unstable/amd64 on profitbricks-build1-amd64 done
+ echo 'Sat Sep 5 22:54:42 UTC 2015 - build #1 for mrbayes/unstable/amd64 on profitbricks-build1-amd64 done'
+ exit 0
+ cleanup_all
+ '[' 0 -eq 1 ']'
+ '[' '' = failure ']'
+ '[' '!' -z '' ']'
+ gzip -9fvn /srv/reproducible-results/tmp.YtidnVbwiJ/tmp.mgZutmrVK0
/srv/reproducible-results/tmp.YtidnVbwiJ/tmp.mgZutmrVK0: 81.1% -- replaced with /srv/reproducible-results/tmp.YtidnVbwiJ/tmp.mgZutmrVK0.gz
+ '[' 1 = legacy ']'
+ '[' 1 = ng ']'
+ false
+ rm -f /tmp/reproducible-lockfile-unstable-amd64-mrbayes
Sat Sep 5 22:54:42 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-akttS5mJ, which will now be removed.
+ rsync -e 'ssh -p 22' -r profitbricks-build1-amd64.debian.net:/srv/reproducible-results/tmp.aRmAOjkTW3/b1 /srv/reproducible-results/tmp.aRmAOjkTW3/
jenkins_node_wrapper.sh[39837] remote_host called with rsync --server --sender -re.iLsfx . /srv/reproducible-results/tmp.aRmAOjkTW3/b1
+ ls -R /srv/reproducible-results/tmp.aRmAOjkTW3
/srv/reproducible-results/tmp.aRmAOjkTW3:
b1
b2
mrbayes_3.2.5+dfsg-1.debian.tar.xz
mrbayes_3.2.5+dfsg-1.dsc
mrbayes_3.2.5+dfsg.orig.tar.xz
tmp.vGh1RkqAgI
/srv/reproducible-results/tmp.aRmAOjkTW3/b1:
build.log
mrbayes-dbg_3.2.5+dfsg-2_amd64.deb
mrbayes-doc_3.2.5+dfsg-2_all.deb
mrbayes-mpi_3.2.5+dfsg-2_amd64.deb
mrbayes_3.2.5+dfsg-2.debian.tar.xz
mrbayes_3.2.5+dfsg-2.dsc
mrbayes_3.2.5+dfsg-2_amd64.buildinfo
mrbayes_3.2.5+dfsg-2_amd64.changes
mrbayes_3.2.5+dfsg-2_amd64.deb
mrbayes_3.2.5+dfsg.orig.tar.xz
/srv/reproducible-results/tmp.aRmAOjkTW3/b2:
+ ssh -p 22 profitbricks-build1-amd64.debian.net 'rm -r /srv/reproducible-results/tmp.aRmAOjkTW3'
jenkins_node_wrapper.sh[39847] remote_host called with rm -r /srv/reproducible-results/tmp.aRmAOjkTW3
+ '[' '!' -f b1/mrbayes_3.2.5+dfsg-1_amd64.changes ']'
+ '[' -f b1/mrbayes_3.2.5+dfsg-2_amd64.changes ']'
+ tee -a /srv/reproducible-results/tmp.aRmAOjkTW3/tmp.vGh1RkqAgI
+ echo 'Version mismatch between main node and first build node, aborting. Please upgrade the schroots...'
Version mismatch between main node and first build node, aborting. Please upgrade the schroots...
+ FTBFS=0
+ calculate_build_duration
++ date +%s
+ END=1441493525
+ DURATION=186
+ update_db_and_html depwait
+ STATUS=depwait
+ '[' -z 3.2.5+dfsg-1 ']'
++ sqlite3 -init /var/lib/jenkins/reproducible.init /var/lib/jenkins/reproducible.db 'SELECT status FROM results WHERE package_id='\''13133'\'''
+ local OLD_STATUS=reproducible
+ '[' reproducible = reproducible ']'
+ '[' depwait '!=' depwait ']'
+ '[' reproducible '!=' depwait ']'
+ '[' 0 -eq 1 ']'
+ sqlite3 -init /var/lib/jenkins/reproducible.init /var/lib/jenkins/reproducible.db 'REPLACE INTO results (package_id, version, status, build_date, build_duration, builder) VALUES ('\''13133'\'', '\''3.2.5+dfsg-1'\'', '\''depwait'\'', '\''2015-09-05 22:48'\'', '\''186'\'', '\''amd64_5/1368'\'')'
+ '[' '!' -z 186 ']'
+ sqlite3 -init /var/lib/jenkins/reproducible.init /var/lib/jenkins/reproducible.db 'INSERT INTO stats_build (name, version, suite, architecture, status, build_date, build_duration, builder) VALUES ('\''mrbayes'\'', '\''3.2.5+dfsg-1'\'', '\''unstable'\'', '\''amd64'\'', '\''depwait'\'', '\''2015-09-05 22:48'\'', '\''186'\'', '\''amd64_5/1368'\'')'
+ sqlite3 -init /var/lib/jenkins/reproducible.init /var/lib/jenkins/reproducible.db 'DELETE FROM schedule WHERE package_id='\''13133'\'';'
+ gen_package_html mrbayes
+ cd /srv/jenkins/bin
+ python3 -c 'import reproducible_html_packages as rep
pkg = rep.Package('\''mrbayes'\'', no_notes=True)
rep.gen_packages_html([pkg], no_clean=True)'
INFO: Starting at 2015-09-05 22:52:05.789152
INFO: Finished at 2015-09-05 22:52:05.794564, took: 0:00:00.005418
+ cd -
+ echo
+ echo 'Successfully updated the database and updated https://reproducible.debian.net/rb-pkg/unstable/amd64/mrbayes.html'
Successfully updated the database and updated https://reproducible.debian.net/rb-pkg/unstable/amd64/mrbayes.html
+ echo
+ exit 1
+ cleanup_all
+ '[' 0 -eq 1 ']'
+ '[' '' = failure ']'
+ '[' '!' -z '' ']'
+ gzip -9fvn /srv/reproducible-results/tmp.aRmAOjkTW3/tmp.vGh1RkqAgI
/srv/reproducible-results/tmp.aRmAOjkTW3/tmp.vGh1RkqAgI: 43.3% -- replaced with /srv/reproducible-results/tmp.aRmAOjkTW3/tmp.vGh1RkqAgI.gz
+ '[' ng = legacy ']'
+ '[' ng = ng ']'
+ gen_package_html mrbayes
+ cd /srv/jenkins/bin
+ python3 -c 'import reproducible_html_packages as rep
pkg = rep.Package('\''mrbayes'\'', no_notes=True)
rep.gen_packages_html([pkg], no_clean=True)'
INFO: Starting at 2015-09-05 22:52:05.966300
INFO: Finished at 2015-09-05 22:52:05.972694, took: 0:00:00.006403
+ cd -
+ cd
+ rm -r /srv/reproducible-results/tmp.aRmAOjkTW3
+ false
+ rm -f /tmp/reproducible-lockfile-unstable-amd64-mrbayes
Sat 5 Sep 22:52:06 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-RcK00Rub, which will now be removed.
Build step 'Execute shell' marked build as failure
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