[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_17 #2993

jenkins at jenkins.debian.net jenkins at jenkins.debian.net
Sat Jan 9 00:49:06 UTC 2016 

See <https://jenkins.debian.net/job/reproducible_builder_armhf_17/2993/>

------------------------------------------
[...truncated 140 lines...]
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper (>= 9)
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 20741 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
No packages will be installed, upgraded, or removed.
0 packages upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 0 B of archives. After unpacking 0 B will be used.
Writing extended state information...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version (1.20.2-1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying source file
I: copying [profisis_1.0.11-2.dsc]
I: copying [./profisis_1.0.11.orig.tar.gz]
I: copying [./profisis_1.0.11-2.debian.tar.xz]
I: Extracting source
gpgv: keyblock resource `/root/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jan  8 02:54:06 2016 GMT+12 using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./profisis_1.0.11-2.dsc
dpkg-source: info: extracting profisis in profisis-1.0.11
dpkg-source: info: unpacking profisis_1.0.11.orig.tar.gz
dpkg-source: info: unpacking profisis_1.0.11-2.debian.tar.xz
I: Building the package
I: Running cd /build/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent" dpkg-buildpackage -us -uc -b -rfakeroot
dpkg-buildpackage: source package profisis
dpkg-buildpackage: source version 1.0.11-2
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build profisis-1.0.11
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
   dh_clean
 debian/rules build
dh build
   dh_testdir
   dh_auto_configure
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --disable-maintainer-mode --disable-dependency-tracking
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating examples/Makefile
configure: WARNING: unrecognized options: --disable-silent-rules, --disable-maintainer-mode, --disable-dependency-tracking
   dh_auto_build
	make -j1
make[1]: Entering directory '/build/profisis-1.0.11'
Making all in examples
make[2]: Entering directory '/build/profisis-1.0.11/examples'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/profisis-1.0.11/examples'
make[2]: Entering directory '/build/profisis-1.0.11'
sed -e 's|__docdir__|/usr/share/doc/profisis|g;s|__datadir__|/usr/share|g;s|__pkgdatadir__|/usr/share/profisis|g;s|__sysconfdir__|/etc|g;s|__bindir__|/usr/bin|g;s|__VERSION__|1.0.11|g' "profisis" | \
pod2man -c 'User Commands' -r "1.0.11" -name PROFISIS > "profisis.1"
make[2]: Leaving directory '/build/profisis-1.0.11'
make[1]: Leaving directory '/build/profisis-1.0.11'
   dh_auto_test
	make -j1 check
make[1]: Entering directory '/build/profisis-1.0.11'
Making check in examples
make[2]: Entering directory '/build/profisis-1.0.11/examples'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/profisis-1.0.11/examples'
make[2]: Entering directory '/build/profisis-1.0.11'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/build/profisis-1.0.11'
make[1]: Leaving directory '/build/profisis-1.0.11'
 fakeroot debian/rules binary
dh binary
   dh_testroot
   dh_prep
   dh_auto_install
	make -j1 install DESTDIR=/build/profisis-1.0.11/debian/profisis AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/profisis-1.0.11'
Making install in examples
make[2]: Entering directory '/build/profisis-1.0.11/examples'
make[3]: Entering directory '/build/profisis-1.0.11/examples'
make[3]: Nothing to be done for 'install-exec-am'.
 /bin/mkdir -p '/build/profisis-1.0.11/debian/profisis/usr/share/doc/profisis/examples'
 /usr/bin/install -c -m 644 ./3A1P_A.fasta ./3A1P_A.hssp ./3A1P_A.profisis ./3A1P_A.rdbProf '/build/profisis-1.0.11/debian/profisis/usr/share/doc/profisis/examples'
make[3]: Leaving directory '/build/profisis-1.0.11/examples'
make[2]: Leaving directory '/build/profisis-1.0.11/examples'
make[2]: Entering directory '/build/profisis-1.0.11'
make[3]: Entering directory '/build/profisis-1.0.11'
 /bin/mkdir -p '/build/profisis-1.0.11/debian/profisis/usr/bin'
 /usr/bin/install -c profisis '/build/profisis-1.0.11/debian/profisis/usr/bin'
make  install-exec-hook
make[4]: Entering directory '/build/profisis-1.0.11'
sed -i -e 's|__docdir__|/usr/share/doc/profisis|g;s|__datadir__|/usr/share|g;s|__pkgdatadir__|/usr/share/profisis|g;s|__sysconfdir__|/etc|g;s|__bindir__|/usr/bin|g;s|__VERSION__|1.0.11|g' "/build/profisis-1.0.11/debian/profisis/usr/bin/profisis"
make[4]: Leaving directory '/build/profisis-1.0.11'
 /bin/mkdir -p '/build/profisis-1.0.11/debian/profisis/usr/share/profisis'
 /usr/bin/install -c -m 644 jctAuto9newHssp990-51 profisisrc.default '/build/profisis-1.0.11/debian/profisis/usr/share/profisis'
 /bin/mkdir -p '/build/profisis-1.0.11/debian/profisis/usr/share/man/man1'
 /usr/bin/install -c -m 644 profisis.1 '/build/profisis-1.0.11/debian/profisis/usr/share/man/man1'
make  install-data-hook
make[4]: Entering directory '/build/profisis-1.0.11'
find '/build/profisis-1.0.11/debian/profisis/usr/share/profisis/profisisrc.default' -type f -exec sed -i -e 's|__datadir__|/usr/share|g;s|__docdir__|/usr/share/doc/profisis|g;s|__pkgdatadir__|/usr/share/profisis|g;s|__sysconfdir__|/etc|g;' '{}' \;
make[4]: Leaving directory '/build/profisis-1.0.11'
make[3]: Leaving directory '/build/profisis-1.0.11'
make[2]: Leaving directory '/build/profisis-1.0.11'
make[1]: Leaving directory '/build/profisis-1.0.11'
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_perl
   dh_link
   dh_strip_nondeterminism
   debian/rules override_dh_compress
make[1]: Entering directory '/build/profisis-1.0.11'
dh_compress -Xexamples/3A1P_A.fasta -Xexamples/3A1P_A.hssp -Xexamples/3A1P_A.rdbProf
make[1]: Leaving directory '/build/profisis-1.0.11'
   dh_fixperms
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'profisis' in '../profisis_1.0.11-2_all.deb'.
 dpkg-genbuildinfo  >../profisis_1.0.11-2_armhf.buildinfo
 dpkg-distaddfile profisis_1.0.11-2_armhf.buildinfo science optional
dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe
 dpkg-genchanges -b >../profisis_1.0.11-2_armhf.changes
dpkg-genchanges: binary-only upload (no source code included)
 dpkg-source --after-build profisis-1.0.11
dpkg-buildpackage: binary-only upload (no source included)
I: copying local configuration
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 /srv/workspace/pbuilder/32660 and its subdirectories
I: Current time: Fri Jan  8 12:48:01 GMT+12 2016
I: pbuilder-time-stamp: 1452300481
+ PRESULT=0
+ '[' 0 -eq 124 ']'
+ false
+ set +x
Sat Jan  9 00:48:01 UTC 2016 - build #1 for profisis/unstable/armhf on odxu4c done.
/srv/reproducible-results/rbuild-debian-MdJ0NJHL/tmp.oy7hfMSchg:	 72.2% -- replaced with /srv/reproducible-results/rbuild-debian-MdJ0NJHL/tmp.oy7hfMSchg.gz
Sat Jan  9 00:48:01 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-53v580zT, which will now be removed.
/srv/reproducible-results/rbuild-debian-XPpXzanx:
total 16
drwxr-xr-x 2 jenkins jenkins 4096 Jan  9 00:48 b1
drwxr-xr-x 2 jenkins jenkins 4096 Jan  9 00:45 b2
-rw-r--r-- 1 jenkins jenkins 2045 Jan  8 14:57 profisis_1.0.11-2.dsc
-rw------- 1 jenkins jenkins 2754 Jan  9 00:45 tmp.F16JJ4Ma72

/srv/reproducible-results/rbuild-debian-XPpXzanx/b1:
total 244
-rw-r--r-- 1 jenkins jenkins   9522 Jan  9 00:48 build.log
-rw-r--r-- 1 jenkins jenkins   2988 Jan  9 00:48 profisis_1.0.11-2.debian.tar.xz
-rw-r--r-- 1 jenkins jenkins   2045 Jan  9 00:48 profisis_1.0.11-2.dsc
-rw-r--r-- 1 jenkins jenkins  62530 Jan  9 00:48 profisis_1.0.11-2_all.deb
-rw-r--r-- 1 jenkins jenkins   4177 Jan  9 00:48 profisis_1.0.11-2_armhf.buildinfo
-rw-r--r-- 1 jenkins jenkins   1178 Jan  9 00:48 profisis_1.0.11-2_armhf.changes
-rw-r--r-- 1 jenkins jenkins 142999 Jan  9 00:48 profisis_1.0.11.orig.tar.gz

/srv/reproducible-results/rbuild-debian-XPpXzanx/b2:
total 0
====================================================================================

Sat Jan  9 00:48:14 UTC 2016 - running /srv/jenkins/bin/reproducible_build.sh () on hb0 now.

To learn to understand this, clone git.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 profisis unstable /srv/reproducible-results/rbuild-debian-XPpXzanx" as arguments.

====================================================================================
Sat Jan  9 00:48:14 UTC 2016 - start running "/srv/jenkins/bin/reproducible_build.sh" (md5sum 0a605f8a4afe4c6dbeabdf412e13bc51) as "/tmp/jenkins-script-mg6HkuT4" on hb0.

Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'profisis' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/profisis/trunk/
Need to get 148 kB of source archives.
Get:1 http://ftp.us.debian.org/debian unstable/main profisis 1.0.11-2 (dsc) [2045 B]
Get:2 http://ftp.us.debian.org/debian unstable/main profisis 1.0.11-2 (tar) [143 kB]
Get:3 http://ftp.us.debian.org/debian unstable/main profisis 1.0.11-2 (diff) [2988 B]
Fetched 148 kB in 0s (2875 kB/s)
Download complete and in download only mode
=============================================================================
Re-Building profisis in unstable on armhf on hb0-armhf-rb.debian.net now.
Date:     Sat Jan  9 00:48:17 UTC 2016
Date UTC: Sat Jan  9 00:48:17 UTC 2016
=============================================================================
++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian-XPpXzanx
+ local TMPCFG=/srv/reproducible-results/rbuild-debian-XPpXzanx/pbuilderrc_BQfS
+ NEW_NUM_CPU=2
+ '[' armhf = armhf ']'
++ bc
++ echo 2-1
+ NEW_NUM_CPU=1
+ cat
+ set +e
+ sudo timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian-XPpXzanx/pbuilderrc_BQfS --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian-XPpXzanx/b2 --logfile b2/build.log profisis_1.0.11-2.dsc
W: /root/.pbuilderrc does not exist
/srv/reproducible-results/rbuild-debian-XPpXzanx/pbuilderrc_BQfS: line 6: warning: setlocale: LC_ALL: cannot change locale (fr_CH.UTF-8): No such file or directory
I: Logging to b2/build.log
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Jan  9 14:48:18 GMT-14 2016
I: pbuilder-time-stamp: 1452300498
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
Terminated
Sat  9 Jan 00:49:05 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-o4VWUeLC, which will now be removed.
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:537)
	at hudson.model.Run.execute(Run.java:1741)
	at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
	at hudson.model.ResourceController.execute(ResourceController.java:98)
	at hudson.model.Executor.run(Executor.java:408)

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