[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_9 #60860
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Fri Dec 2 12:14:58 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_9/60860/------------------------------------------
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Setting up xauth (1:1.0.9-1) ...
Setting up libpango-1.0-0:amd64 (1.40.3-3) ...
Setting up libcairo2:amd64 (1.14.6-1.1) ...
Setting up libcurl3:amd64 (7.50.1-1) ...
Setting up libtk8.6:amd64 (8.6.6-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.40.3-3) ...
Setting up libpangocairo-1.0-0:amd64 (1.40.3-3) ...
Setting up r-base-core (3.3.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-littler (0.3.1-1) ...
Setting up littler (0.3.1-1) ...
Setting up r-cran-gtable (0.2.0-1) ...
Setting up r-base-dev (3.3.2-1) ...
Setting up r-cran-assertthat (0.1-1) ...
Setting up r-cran-rcolorbrewer (1.1-2-1) ...
Setting up r-cran-registry (0.3-1) ...
Setting up r-cran-gridbase (0.4-7-2) ...
Setting up r-cran-stringi (1.1.2-1) ...
Setting up r-cran-pkgkitten (0.1.4-1) ...
Setting up r-cran-rcpp (0.12.8-1) ...
Setting up r-cran-labeling (0.3-1) ...
Setting up r-cran-colorspace (1.2-7-1) ...
Setting up r-cran-mass (7.3-45-1) ...
Setting up r-cran-plyr (1.8.4-1) ...
Setting up r-cran-digest (0.6.10-1) ...
Setting up r-cran-xtable (1:1.8-2-1) ...
Setting up r-cran-magrittr (1.5-3) ...
Setting up r-cran-cluster (2.0.5-1) ...
Setting up r-cran-dichromat (2.0.0-3) ...
Setting up r-cran-xml (3.98-1.5-1) ...
Setting up r-cran-codetools (0.2-15-1) ...
Setting up r-cran-iterators (1.0.8-1) ...
Setting up r-cran-lattice (0.20-34-1) ...
Setting up r-cran-lazyeval (0.2.0-1) ...
Setting up r-cran-stringr (1.1.0-1) ...
Setting up r-cran-foreach (1.4.3-1) ...
Setting up r-cran-pkgmaker (0.22-1) ...
Setting up r-cran-munsell (0.4.3-1) ...
Setting up r-cran-rngtools (1.2.4-2) ...
Setting up r-cran-doparallel (1.0.10-3) ...
Setting up r-cran-reshape2 (1.4.2-1) ...
Setting up r-cran-scales (0.4.1-1) ...
Setting up r-cran-tibble (1.2-1) ...
Setting up r-cran-matrix (1.2-7.1-1) ...
Setting up r-cran-irlba (2.1.2-1) ...
Setting up r-cran-ggplot2 (2.2.0-1) ...
Setting up r-cran-nmf (0.20.6-1) ...
Setting up r-cran-igraph (1.0.1-1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up dh-r (20160916) ...
Processing triggers for libc-bin (2.24-7) ...
Processing triggers for ca-certificates (20161102) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
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 (1.21-2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying source file
I: copying [r-cran-boolnet_2.1.3-1.dsc]
I: copying [./r-cran-boolnet_2.1.3.orig.tar.gz]
I: copying [./r-cran-boolnet_2.1.3-1.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Nov 26 11:06:04 2016 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille at debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-cran-boolnet_2.1.3-1.dsc
dpkg-source: info: extracting r-cran-boolnet in r-cran-boolnet-2.1.3
dpkg-source: info: unpacking r-cran-boolnet_2.1.3.orig.tar.gz
dpkg-source: info: unpacking r-cran-boolnet_2.1.3-1.debian.tar.xz
I: Building the package
I: Running cd /build/*/ && 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 r-cran-boolnet
dpkg-buildpackage: info: source version 2.1.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-cran-boolnet-2.1.3
dpkg-buildpackage: info: host architecture amd64
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build
make: 'build' is up to date.
fakeroot debian/rules binary
dh binary --buildsystem R
dh_testdir -O--buildsystem=R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
dh_installdirs -O--buildsystem=R
dh_auto_install -O--buildsystem=R
I: R Package: BoolNet Version: 2.1.3
I: Building using R version 3.3.2-1
I: R API version: r-api-3
I: Using built-time from d/changelog: Sat, 26 Nov 2016 23:52:07 +0100
mkdir -p /build/r-cran-boolnet-2.1.3/debian/r-cran-boolnet/usr/lib/R/site-library
R CMD INSTALL -l /build/r-cran-boolnet-2.1.3/debian/r-cran-boolnet/usr/lib/R/site-library --clean . "--built-timestamp='Sat, 26 Nov 2016 23:52:07 +0100'"
* installing *source* package 'BoolNet' ...
** package 'BoolNet' successfully unpacked and MD5 sums checked
** libs
make[1]: Entering directory '/build/r-cran-boolnet-2.1.3/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attractor_info.c -o attractor_info.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attractor_search_interface.c -o attractor_search_interface.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.c -o common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c picosat.c -o picosat.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c probabilistic_boolean_network.c -o probabilistic_boolean_network.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c reconstruct_network.c -o reconstruct_network.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sat_search.c -o sat_search.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c statespace_search.c -o statespace_search.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c symbolic_network.c -o symbolic_network.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c symbolic_simulator.c -o symbolic_simulator.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o BoolNet.so attractor_info.o attractor_search_interface.o common.o picosat.o probabilistic_boolean_network.o reconstruct_network.o sat_search.o statespace_search.o symbolic_network.o symbolic_simulator.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/build/r-cran-boolnet-2.1.3/src'
make[1]: Entering directory '/build/r-cran-boolnet-2.1.3/src'
make[1]: Leaving directory '/build/r-cran-boolnet-2.1.3/src'
installing to /build/r-cran-boolnet-2.1.3/debian/r-cran-boolnet/usr/lib/R/site-library/BoolNet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BoolNet)
I: Using r-cran-igraph for Imports:igraph (>= 0.6)
I: Using r-cran-xml for Imports:XML
dh_install -O--buildsystem=R
dh_installdocs -O--buildsystem=R
dh_installchangelogs -O--buildsystem=R
dh_installexamples -O--buildsystem=R
dh_installman -O--buildsystem=R
dh_installcatalogs -O--buildsystem=R
dh_installcron -O--buildsystem=R
dh_installdebconf -O--buildsystem=R
dh_installemacsen -O--buildsystem=R
dh_installifupdown -O--buildsystem=R
dh_installinfo -O--buildsystem=R
dh_systemd_enable -O--buildsystem=R
dh_installinit -O--buildsystem=R
dh_systemd_start -O--buildsystem=R
dh_installmenu -O--buildsystem=R
dh_installmime -O--buildsystem=R
dh_installmodules -O--buildsystem=R
dh_installlogcheck -O--buildsystem=R
dh_installlogrotate -O--buildsystem=R
dh_installpam -O--buildsystem=R
dh_installppp -O--buildsystem=R
dh_installudev -O--buildsystem=R
dh_installgsettings -O--buildsystem=R
dh_bugfiles -O--buildsystem=R
dh_ucf -O--buildsystem=R
dh_lintian -O--buildsystem=R
dh_gconf -O--buildsystem=R
dh_icons -O--buildsystem=R
dh_perl -O--buildsystem=R
dh_usrlocal -O--buildsystem=R
dh_link -O--buildsystem=R
dh_installwm -O--buildsystem=R
dh_installxfonts -O--buildsystem=R
dh_strip_nondeterminism -O--buildsystem=R
dh_compress -O--buildsystem=R
dh_fixperms -O--buildsystem=R
dh_strip -O--buildsystem=R
dh_makeshlibs -O--buildsystem=R
dh_shlibdeps -O--buildsystem=R
dh_installdeb -O--buildsystem=R
dh_gencontrol -O--buildsystem=R
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--buildsystem=R
dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-cran-boolnet-dbgsym' in '../r-cran-boolnet-dbgsym_2.1.3-1_amd64.deb'.
dpkg-deb: building package 'r-cran-boolnet' in '../r-cran-boolnet_2.1.3-1_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=binary >../r-cran-boolnet_2.1.3-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build r-cran-boolnet-2.1.3
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/25372 and its subdirectories
I: Current time: Fri Dec 2 00:12:57 -12 2016
I: pbuilder-time-stamp: 1480680777
151c151
< libperl5.24 (= 5.24.1~rc4-1),
---
> libperl5.24 (= 5.24.1~rc3-3),
220,222c220,222
< perl (= 5.24.1~rc4-1),
< perl-base (= 5.24.1~rc4-1),
< perl-modules-5.24 (= 5.24.1~rc4-1),
---
> perl (= 5.24.1~rc3-3),
> perl-base (= 5.24.1~rc3-3),
> perl-modules-5.24 (= 5.24.1~rc3-3),
Error: database is locked
/srv/reproducible-results/rbuild-debian-eZJWc8Oh/tmp.UAF1rqmkyZ: 81.9% -- replaced with /srv/reproducible-results/rbuild-debian-eZJWc8Oh/tmp.UAF1rqmkyZ.gz
INFO: Starting at 2016-12-02 12:13:58.325230
CRITICAL: SQLite database locked, could not execute query:
CRITICAL: "SELECT r.status, r.version, r.build_date
CRITICAL: FROM results AS r JOIN sources AS s
CRITICAL: ON r.package_id=s.id WHERE s.name='r-cran-boolnet'
CRITICAL: AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-02 12:14:58.431367, took: 0:01:00.106163
Warning: cannot update html pages for r-cran-boolnet
Fri 2 Dec 12:14:58 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-z1s9jhUI, which will now be removed.
Build step 'Execute shell' marked build as failure
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