[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_i386_11 #25737
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Thu Dec 15 12:19:16 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_i386_11/25737/------------------------------------------
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Setting up r-cran-mass (7.3-45-1) ...
Setting up r-cran-plyr (1.8.4-1) ...
Setting up r-cran-rcurl (1.95-4.8-1) ...
Setting up r-cran-mime (0.4-2) ...
Setting up r-cran-yaml (2.1.13-5) ...
Setting up r-cran-digest (0.6.10-1) ...
Setting up r-cran-rsqlite (1.0.0-2) ...
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-data.table (1.10.0-1) ...
Setting up r-cran-dichromat (2.0.0-3) ...
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-highr (0.6-1) ...
Setting up r-cran-chron (2.3-47-2) ...
Setting up r-cran-formula (1.2-1-1) ...
Setting up r-cran-lattice (0.20-34-1) ...
Setting up r-cran-lazyeval (0.2.0-1) ...
Setting up r-cran-latticeextra (0.6-28-2) ...
Setting up r-cran-foreign (0.8.67-1) ...
Setting up r-cran-stringr (1.1.0-1) ...
Setting up r-cran-markdown (0.7.7-1) ...
Setting up r-cran-evaluate (0.10-1) ...
Setting up r-cran-rcpparmadillo (0.7.500.0.0-1) ...
Setting up r-cran-munsell (0.4.3-1) ...
Setting up r-cran-futile.logger (1.4.3-1) ...
Setting up r-cran-reshape2 (1.4.2-1) ...
Setting up r-bioc-iranges (2.8.1-1) ...
Setting up r-cran-scales (0.4.1-1) ...
Setting up r-cran-tibble (1.2-1) ...
Setting up r-bioc-biocparallel (1.8.0-2) ...
Setting up r-cran-matrix (1.2-7.1-1) ...
Setting up r-bioc-genomeinfodb (1.10.1-1) ...
Setting up r-cran-knitr (1.15.1-1) ...
Setting up r-bioc-xvector (0.14.0-1) ...
Setting up r-bioc-annotationdbi (1.36.0-1) ...
Setting up r-cran-ggplot2 (2.2.0-1) ...
Setting up r-cran-survival (2.40-1-1) ...
Setting up r-bioc-genomicranges (1.26.1-1) ...
Setting up r-bioc-annotate (1.52.0+dfsg-1) ...
Setting up r-bioc-summarizedexperiment (1.4.0-1) ...
Setting up r-bioc-genefilter (1.56.0-1) ...
Setting up r-cran-rpart (4.1-10-2) ...
Setting up r-bioc-geneplotter (1.52.0-1) ...
Setting up r-cran-hmisc (3.17-4-2) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10.2.2) ...
Setting up dh-r (20161130) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
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=i386 -rfakeroot
dpkg-buildpackage: warning: --buildinfo-id is deprecated, it is without effect
dpkg-buildpackage: info: source package r-bioc-deseq2
dpkg-buildpackage: info: source version 1.14.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-bioc-deseq2-1.14.1
dpkg-buildpackage: info: host architecture i386
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: DESeq2 Version: 1.14.1
I: Building using R version 3.3.2-1
I: R API version: r-api-3
I: Using built-time from d/changelog: Sun, 04 Dec 2016 14:11:45 +0100
mkdir -p /build/r-bioc-deseq2-1.14.1/debian/r-bioc-deseq2/usr/lib/R/site-library
R CMD INSTALL -l /build/r-bioc-deseq2-1.14.1/debian/r-bioc-deseq2/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 04 Dec 2016 14:11:45 +0100'"
* installing *source* package 'DESeq2' ...
** libs
make[1]: Entering directory '/build/r-bioc-deseq2-1.14.1/src'
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -I"/usr/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c DESeq2.cpp -o DESeq2.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -I"/usr/lib/R/site-library/RcppArmadillo/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-PAdLwq/r-base-3.3.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o DESeq2.so DESeq2.o RcppExports.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/build/r-bioc-deseq2-1.14.1/src'
make[1]: Entering directory '/build/r-bioc-deseq2-1.14.1/src'
make[1]: Leaving directory '/build/r-bioc-deseq2-1.14.1/src'
installing to /build/r-bioc-deseq2-1.14.1/debian/r-bioc-deseq2/usr/lib/R/site-library/DESeq2/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DESeq2)
I: Using r-bioc-s4vectors for Depends:S4Vectors (>= 0.9.25)
I: Using r-bioc-iranges for Depends:IRanges
I: Using r-bioc-genomicranges for Depends:GenomicRanges
I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 1.1.6)
I: Using r-cran-testthat for Suggests:testthat
I: Using r-cran-knitr for Suggests:knitr
W: Cannot find a debian package for Suggests:BiocStyle
W: Cannot find a debian package for Suggests:vsn
I: Using r-cran-pheatmap for Suggests:pheatmap
I: Using r-cran-rcolorbrewer for Suggests:RColorBrewer
W: Cannot find a debian package for Suggests:airway
W: Cannot find a debian package for Suggests:IHW
W: Cannot find a debian package for Suggests:tximport
W: Cannot find a debian package for Suggests:tximportData
W: Cannot find a debian package for Suggests:readr
W: Cannot find a debian package for Suggests:pasilla (>= 0.2.10)
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.7.5)
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-biocparallel for Imports:BiocParallel
I: Using r-bioc-genefilter for Imports:genefilter
I: Using r-bioc-geneplotter for Imports:geneplotter
I: Using r-cran-ggplot2 for Imports:ggplot2
I: Using r-cran-hmisc for Imports:Hmisc
I: Using r-cran-rcpp for Imports:Rcpp (>= 0.11.0)
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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-deseq2/usr/lib/R/site-library/DESeq2/libs/DESeq2.so was not linked against libgfortran.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-deseq2/usr/lib/R/site-library/DESeq2/libs/DESeq2.so was not linked against libquadmath.so.0 (it uses none of the library's symbols)
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-deseq2-dbgsym' in '../r-bioc-deseq2-dbgsym_1.14.1-1_i386.deb'.
dpkg-deb: building package 'r-bioc-deseq2' in '../r-bioc-deseq2_1.14.1-1_i386.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-deseq2_1.14.1-1_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-deseq2-1.14.1
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/8368 and its subdirectories
I: Current time: Thu Dec 15 00:16:34 -12 2016
I: pbuilder-time-stamp: 1481804194
168c168
< libsepol1 (= 2.6-2),
---
> libsepol1 (= 2.6-1),
210c210
< linux-libc-dev (= 4.8.11-1),
---
> linux-libc-dev (= 4.8.7-1),
249c249
< r-cran-data.table (= 1.10.0-1),
---
> r-cran-data.table (= 1.9.6-1),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-wHtwuIZR/tmp.dEFAsiKAXU: 81.9% -- replaced with /srv/reproducible-results/rbuild-debian-wHtwuIZR/tmp.dEFAsiKAXU.gz
INFO: Starting at 2016-12-15 12:18:15.920890
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-deseq2'
CRITICAL: AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-15 12:19:16.026193, took: 0:01:00.105331
Warning: cannot update html pages for r-bioc-deseq2
All cleanup done.
Thu 15 Dec 12:19:16 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-4pQNtwkR, which will now be removed.
Build step 'Execute shell' marked build as failure
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