[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_2 #62381
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Wed Dec 7 13:38:28 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_2/62381/------------------------------------------
[...truncated 5606 lines...]
Setting up r-bioc-biocgenerics (0.20.0-1) ...
Setting up r-bioc-biobase (2.34.0-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-cran-dbi (0.5-1-1) ...
Setting up r-cran-futile.options (1.0.0-2) ...
Setting up r-cran-rcurl (1.95-4.8-1) ...
Setting up r-cran-rsqlite (1.0.0-2) ...
Setting up r-cran-lambda.r (1.1.9-1) ...
Setting up r-cran-snow (1:0.4.2-1) ...
Setting up r-bioc-s4vectors (0.12.0-1) ...
Setting up r-cran-xml (3.98-1.5-1) ...
Setting up r-cran-lattice (0.20-34-1) ...
Setting up r-cran-futile.logger (1.4.3-1) ...
Setting up r-bioc-iranges (2.8.0-1) ...
Setting up r-bioc-biocparallel (1.8.0-2) ...
Setting up r-cran-matrix (1.2-7.1-1) ...
Setting up r-bioc-genomeinfodb (1.10.0-1) ...
Setting up r-bioc-xvector (0.14.0-1) ...
Setting up r-bioc-biostrings (2.42.0-1) ...
Setting up r-bioc-annotationdbi (1.36.0-1) ...
Setting up r-bioc-genomicranges (1.26.1-1) ...
Setting up r-bioc-summarizedexperiment (1.4.0-1) ...
Setting up r-bioc-biomart (2.30.0-1) ...
Setting up r-bioc-rsamtools (1.26.1-1) ...
Setting up r-bioc-genomicalignments (1.10.0-1) ...
Setting up r-bioc-rtracklayer (1.34.0-2) ...
Setting up r-bioc-genomicfeatures (1.26.0-1) ...
Setting up r-bioc-bsgenome (1.42.0-2) ...
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: 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-bioc-variantannotation
dpkg-buildpackage: info: source version 1.20.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-bioc-variantannotation-1.20.1
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: VariantAnnotation Version: 1.20.1
I: Building using R version 3.3.2-1
I: R API version: r-api-3
I: Using built-time from d/changelog: Wed, 30 Nov 2016 10:35:23 +0100
mkdir -p /build/r-bioc-variantannotation-1.20.1/debian/r-bioc-variantannotation/usr/lib/R/site-library
R CMD INSTALL -l /build/r-bioc-variantannotation-1.20.1/debian/r-bioc-variantannotation/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 30 Nov 2016 10:35:23 +0100'"
* installing *source* package 'VariantAnnotation' ...
** libs
make[1]: Entering directory '/build/r-bioc-variantannotation-1.20.1/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 rle.c -o rle.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 strhash.c -o strhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 utilities.c -o utilities.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 vcffile.c -o vcffile.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 vcftype.c -o vcftype.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/Rsamtools/include" -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 writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/build/r-bioc-variantannotation-1.20.1/src'
make[1]: Entering directory '/build/r-bioc-variantannotation-1.20.1/src'
make[1]: Leaving directory '/build/r-bioc-variantannotation-1.20.1/src'
installing to /build/r-bioc-variantannotation-1.20.1/debian/r-bioc-variantannotation/usr/lib/R/site-library/VariantAnnotation/libs
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantAnnotation)
W: Ignoring specified R dependency: R (>= 2.8.0)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.3)
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.7.1)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.19.47)
I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 0.3.1)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.23.10)
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-annotationhub for Suggests:AnnotationHub
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene
W: Cannot find a debian package for Suggests:SNPlocs.Hsapiens.dbSNP.20110815
W: Cannot find a debian package for Suggests:SNPlocs.Hsapiens.dbSNP.20101109
W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP132
W: Cannot find a debian package for Suggests:SIFT.Hsapiens.dbSNP137
W: Cannot find a debian package for Suggests:PolyPhen.Hsapiens.dbSNP131
I: Using r-bioc-snpstats for Suggests:snpStats
I: Using r-cran-ggplot2 for Suggests:ggplot2
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-dbi for Imports:DBI
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.9.47)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.3.25)
I: Using r-bioc-xvector for Imports:XVector (>= 0.5.6)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.33.5)
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.27.9)
I: Using r-bioc-bsgenome for Imports:BSgenome (>= 1.37.6)
I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.25.16)
I: Using r-bioc-genomicfeatures for Imports:GenomicFeatures (>= 1.19.17)
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-bioc-variantannotation-dbgsym' in '../r-bioc-variantannotation-dbgsym_1.20.1-1_amd64.deb'.
dpkg-deb: building package 'r-bioc-variantannotation' in '../r-bioc-variantannotation_1.20.1-1_amd64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=binary >../r-bioc-variantannotation_1.20.1-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-variantannotation-1.20.1
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/30086 and its subdirectories
I: Current time: Tue Jan 9 07:59:02 -12 2018
I: pbuilder-time-stamp: 1515527942
9c9
< binutils (= 2.27.51.20161127-1),
---
> binutils (= 2.27.51.20161201-1),
25c25
< dh-r (= 20160916),
---
> dh-r (= 20161130),
176c176
< libsystemd0 (= 232-6),
---
> libsystemd0 (= 232-7),
189c189
< libudev1 (= 232-6),
---
> libudev1 (= 232-7),
233c233
< r-bioc-genomeinfodb (= 1.10.0-1),
---
> r-bioc-genomeinfodb (= 1.10.1-1),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-GSyLsF0b/tmp.4yNWYkxNaS: 82.4% -- replaced with /srv/reproducible-results/rbuild-debian-GSyLsF0b/tmp.4yNWYkxNaS.gz
INFO: Starting at 2016-12-07 13:37:28.260547
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-bioc-variantannotation'
CRITICAL: AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-07 13:38:28.397790, took: 0:01:00.137293
Warning: cannot update html pages for r-bioc-variantannotation
All cleanup done.
Wed 7 Dec 13:38:28 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-uxeklVAR, which will now be removed.
Build step 'Execute shell' marked build as failure
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