[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_29 #7026
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Fri Dec 23 16:31:13 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_29/7026/------------------------------------------
[...truncated 2018 lines...]
Setting up openjdk-8-jdk-headless:amd64 (8u111-b14-3) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/idlj to provide /usr/bin/idlj (idlj) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsimport to provide /usr/bin/wsimport (wsimport) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/rmic to provide /usr/bin/rmic (rmic) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jsadebugd to provide /usr/bin/jsadebugd (jsadebugd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/native2ascii to provide /usr/bin/native2ascii (native2ascii) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javah to provide /usr/bin/javah (javah) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jhat to provide /usr/bin/jhat (jhat) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/xjc to provide /usr/bin/xjc (xjc) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/schemagen to provide /usr/bin/schemagen (schemagen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/extcheck to provide /usr/bin/extcheck (extcheck) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/wsgen to provide /usr/bin/wsgen (wsgen) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
Setting up devscripts (2.16.13) ...
Setting up dh-strip-nondeterminism (0.029-1) ...
Setting up maven-repo-helper (1.9.2) ...
Setting up default-jre-headless (2:1.8-57) ...
Setting up default-jdk-headless (2:1.8-57) ...
Setting up debhelper (10.2.2) ...
Setting up javahelper (0.59) ...
Processing triggers for libc-bin (2.24-8) ...
Processing triggers for ca-certificates (20161130) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version (1.21-3).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/1st/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b --buildinfo-id=amd64 -rfakeroot
dpkg-buildpackage: warning: --buildinfo-id is deprecated, it is without effect
dpkg-buildpackage: info: source package libssw
dpkg-buildpackage: info: source version 1.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Sascha Steinbiss <satta at debian.org>
dpkg-source --before-build libssw-1.1
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh clean --with javahelper --with jh_maven_repo_helper
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/1st/libssw-1.1'
rm -f debian/libssw*install debian/libssw*links debian/ssw-align.1
/usr/bin/make -C src clean
make[2]: Entering directory '/build/1st/libssw-1.1/src'
rm -f ssw.o ssw_cpp.o ssw-align libssw.so.0 example_c example_cpp libsswjni.so *.jar ssw/Aligner.class ssw/Alignment.class *~ libssw.a
make[2]: Leaving directory '/build/1st/libssw-1.1/src'
make[1]: Leaving directory '/build/1st/libssw-1.1'
jh_clean
mh_clean
dh_clean
debian/rules build
dh build --with javahelper --with jh_maven_repo_helper
dh_testdir
dh_update_autotools_config
dh_auto_configure
jh_linkjars
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/1st/libssw-1.1'
/usr/bin/make -C src default java
make[2]: Entering directory '/build/1st/libssw-1.1/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -shared -rdynamic -Wl,-soname,libssw.so.0 -o libssw.so.0 ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp -Wl,-z,relro -Wl,-z,now
ln -s libssw.so.0 libssw.so
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security -o ssw-align main.c kseq.h -L. -lssw -lm -lz -Wl,-z,relro -Wl,-z,now
gcc -c -o ssw.o ssw.c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security
gcc -o example_c ssw.o example.c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lz -Wl,-z,relro -Wl,-z,now
g++ -c -o ssw_cpp.o ssw_cpp.cpp -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security
g++ -o example_cpp example.cpp ssw.o ssw_cpp.o -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security -lm -lz -Wl,-z,relro -Wl,-z,now
ar rcs libssw.a ssw.o ssw_cpp.o
javac -target 1.6 -source 1.6 ssw/Aligner.java
warning: [options] bootstrap class path not set in conjunction with -source 1.6
1 warning
jar cvf ssw.jar ssw/Aligner.class ssw/Alignment.class
added manifest
adding: ssw/Aligner.class(in = 2486) (out= 1521)(deflated 38%)
adding: ssw/Alignment.class(in = 1029) (out= 596)(deflated 42%)
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/1st/libssw-1.1=. -fstack-protector-strong -Wformat -Werror=format-security -I"/include" -I"/include/linux" -I/usr/lib/jvm/default-java/include/ -I/usr/lib/jvm/default-java/include/linux -fPIC -shared -rdynamic -o libsswjni.so sswjni.c ssw.c -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/build/1st/libssw-1.1/src'
make[1]: Leaving directory '/build/1st/libssw-1.1'
jh_build
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/1st/libssw-1.1'
src/example_c
optimal_alignment_score: 21 sub-optimal_alignment_score: 8 target_begin: 9 target_end: 22 query_begin: 1 query_end: 15
Target: 9 CTGACCCGG-AAATC 22
||||*||||*|||||
Query: 1 CTGAGCCGGTAAATC 15
src/example_cpp
===== SSW result =====
Best Smith-Waterman score: 21
Next-best Smith-Waterman score: 8
Reference start: 8
Reference end: 21
Query start: 0
Query end: 14
Next-best reference end: 4
Number of mismatches: 2
Cigar: 4=1X4=1I5=
======================
make[1]: Leaving directory '/build/1st/libssw-1.1'
fakeroot debian/rules binary
dh binary --with javahelper --with jh_maven_repo_helper
dh_testroot
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/1st/libssw-1.1'
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw0.install.in > debian/libssw0.install
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-dev.install.in > debian/libssw-dev.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
-e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-dev.links.in > debian/libssw-dev.links
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-java.install.in > debian/libssw-java.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
-e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-java.links.in > debian/libssw-java.links
mv src/ssw.jar src/ssw-1.1.jar
dh_auto_install
make[1]: Leaving directory '/build/1st/libssw-1.1'
dh_install
jh_installjavadoc
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installman
make[1]: Entering directory '/build/1st/libssw-1.1'
LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \
-I debian/extra-man-info.txt \
-N -n 'fast Smith-Waterman aligner' \
--no-discard-stderr src/ssw-align \
| fgrep -v ERROR > debian/ssw-align.1
ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
dh_installman
make[1]: Leaving directory '/build/1st/libssw-1.1'
dh_perl
dh_link
jh_installlibs
jh_classpath
jh_manifest
jh_exec
jh_depends
mh_installpoms
mh_linkjars --skip-clean-poms
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
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
dpkg-gencontrol: warning: Depends field of package libssw-dev: unknown substitution variable ${shlibs:Depends}
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
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums
dh_builddeb
dpkg-deb: building package 'libssw-dev' in '../libssw-dev_1.1-1_amd64.deb'.
dpkg-deb: building package 'libssw0-dbgsym' in '../libssw0-dbgsym_1.1-1_amd64.deb'.
dpkg-deb: building package 'libssw-java-dbgsym' in '../libssw-java-dbgsym_1.1-1_amd64.deb'.
dpkg-deb: building package 'ssw-align-dbgsym' in '../ssw-align-dbgsym_1.1-1_amd64.deb'.
dpkg-deb: building package 'libssw0' in '../libssw0_1.1-1_amd64.deb'.
dpkg-deb: building package 'libssw-java' in '../libssw-java_1.1-1_amd64.deb'.
dpkg-deb: building package 'ssw-align' in '../ssw-align_1.1-1_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=binary >../libssw_1.1-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build libssw-1.1
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
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/13908 and its subdirectories
I: Current time: Fri Dec 23 04:31:10 -12 2016
I: pbuilder-time-stamp: 1482510670
Fri Dec 23 16:31:11 UTC 2016 I: 1st build successful. Starting 2nd build on remote node profitbricks-build5-amd64.debian.net.
Fri Dec 23 16:31:11 UTC 2016 I: Preparing to do remote build '2' on profitbricks-build5-amd64.debian.net.
Fri Dec 23 16:31:11 UTC 2016 - checking if profitbricks-build5-amd64.debian.net is up.
removed ‘/tmp/read-only-fs-test-jg72ZT’
====================================================================================
Thu Jan 25 22:54:12 UTC 2018 - running /srv/jenkins/bin/reproducible_build.sh () on profitbricks-build5-amd64 now.
To learn to understand this, git clone https://anonscm.debian.org/git/qa/jenkins.debian.net.git
and then have a look at the files README, INSTALL, CONTRIBUTING and maybe TODO.
This invocation of this script, which is located in bin/reproducible_build.sh,
has been called using "2 libssw unstable /srv/reproducible-results/rbuild-debian-PMnewGVD 1.1-1" as arguments.
Please send technical feedback about jenkins to qa-jenkins-dev at lists.alioth.debian.org,
feedback about specific jobs result should go to their respective lists and/or the BTS.
====================================================================================
Thu Jan 25 22:54:12 UTC 2018 - start running "/srv/jenkins/bin/reproducible_build.sh" (md5sum 8caef8dffbe5c3041bff5d0cf085aa0c) as "/tmp/jenkins-script-MASOVrcR" on profitbricks-build5-amd64.
Thu Jan 25 22:54:12 UTC 2018 I: Downloading source for unstable/libssw
Reading package lists...
NOTICE: 'libssw' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/libssw.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/libssw.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 12.3 MB of source archives.
Get:1 http://ftp.de.debian.org/debian unstable/main libssw 1.1-1 (dsc) [2298 B]
Get:2 http://ftp.de.debian.org/debian unstable/main libssw 1.1-1 (tar) [12.3 MB]
FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1720)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:404)
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