[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_3 #61006
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Wed Dec 7 13:36:23 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_3/61006/------------------------------------------
[...truncated 6327 lines...]
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-httpuv (1.3.3-3) ...
Setting up r-cran-openssl (0.9.5-1) ...
Setting up r-cran-lattice (0.20-34-1) ...
Setting up r-cran-htmltools (0.3.5-2) ...
Setting up r-cran-shiny (0.14.2+dfsg-1) ...
Setting up r-cran-futile.logger (1.4.3-1) ...
Setting up r-cran-httr (1.2.1-1) ...
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 (1.10.1-1) ...
Setting up r-bioc-xvector (0.14.0-1) ...
Setting up r-bioc-interactivedisplaybase (1.12.0-1) ...
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-annotationhub (2.6.4-1) ...
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 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=amd64 -rfakeroot
dpkg-buildpackage: warning: --buildinfo-id is deprecated, it is without effect
dpkg-buildpackage: info: source package r-bioc-ensembldb
dpkg-buildpackage: info: source version 1.6.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-bioc-ensembldb-1.6.2
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: ensembldb Version: 1.6.2
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 10:33:07 +0100
mkdir -p /build/r-bioc-ensembldb-1.6.2/debian/r-bioc-ensembldb/usr/lib/R/site-library
R CMD INSTALL -l /build/r-bioc-ensembldb-1.6.2/debian/r-bioc-ensembldb/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 30 Nov 2016 10:33:07 +0100'"
* installing *source* package 'ensembldb' ...
** R
** inst
** preparing package for lazy loading
Warning in read.dcf(con) : unable to resolve 'bioconductor.org'
Creating a new generic function for 'transcriptLengths' in package 'ensembldb'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in read.dcf(con) : unable to resolve 'bioconductor.org'
* DONE (ensembldb)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.10)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.23.21)
I: Using r-bioc-genomicfeatures for Depends:GenomicFeatures (>= 1.23.18)
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-knitr for Suggests:knitr
W: Cannot find a debian package for Suggests:rmarkdown
W: Cannot find a debian package for Suggests:EnsDb.Hsapiens.v75 (>= 0.99.7)
I: Using r-cran-runit for Suggests:RUnit
I: Using r-cran-shiny for Suggests:shiny
I: Using r-bioc-gviz for Suggests:Gviz
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
I: Using r-cran-rsqlite for Imports:RSQLite
I: Using r-cran-dbi for Imports:DBI
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.31.19)
I: Using r-bioc-rtracklayer for Imports:rtracklayer
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-annotationhub for Imports:AnnotationHub
I: Using r-bioc-rsamtools for Imports:Rsamtools
I: Using r-bioc-iranges for Imports:IRanges
debian/rules override_dh_install
make[1]: Entering directory '/build/r-bioc-ensembldb-1.6.2'
dh_install
for tst in `grep -H -l 'library(.*EnsDb.Hsapiens.v75.*)' /build/r-bioc-ensembldb-1.6.2/debian/r-bioc-ensembldb/usr/lib/R/site-library/ensembldb/unitTests/test_*.R` ; do rm -f ${tst} ; done
make[1]: Leaving directory '/build/r-bioc-ensembldb-1.6.2'
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
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/r-bioc-ensembldb-1.6.2'
dh_fixperms
find debian -name "*.pl" -exec chmod +x \{\} \;
make[1]: Leaving directory '/build/r-bioc-ensembldb-1.6.2'
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: package r-bioc-ensembldb: unused substitution variable ${perl:Depends}
dh_md5sums -O--buildsystem=R
dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-bioc-ensembldb' in '../r-bioc-ensembldb_1.6.2-1_all.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-ensembldb_1.6.2-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-ensembldb-1.6.2
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/40122 and its subdirectories
I: Current time: Wed Dec 7 01:34:21 -12 2016
I: pbuilder-time-stamp: 1481117661
9c9
< binutils (= 2.27.51.20161201-1),
---
> binutils (= 2.27.51.20161127-1),
25c25
< dh-r (= 20161130),
---
> dh-r (= 20160916),
121c121
< libjs-jquery-ui (= 1.12.1+dfsg-2),
---
> libjs-jquery-ui (= 1.12.1+dfsg-1),
188c188
< libsystemd0 (= 232-7),
---
> libsystemd0 (= 232-6),
201c201
< libudev1 (= 232-7),
---
> libudev1 (= 232-6),
219d218
< libyaml-0-2 (= 0.1.7-2),
241c240
< r-bioc-annotationhub (= 2.6.4-1),
---
> r-bioc-annotationhub (= 2.6.0-1),
248c247
< r-bioc-genomeinfodb (= 1.10.1-1),
---
> r-bioc-genomeinfodb (= 1.10.0-1),
260c259
< r-cran-curl (= 2.3-1),
---
> r-cran-curl (= 2.2-1),
268c267
< r-cran-jsonlite (= 1.1-2),
---
> r-cran-jsonlite (= 1.1-1),
285d283
< r-cran-yaml (= 2.1.13-5),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-hzS1JxTP/tmp.yY9oQMQnGq: 81.9% -- replaced with /srv/reproducible-results/rbuild-debian-hzS1JxTP/tmp.yY9oQMQnGq.gz
INFO: Starting at 2016-12-07 13:35:22.942898
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-ensembldb'
CRITICAL: AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-07 13:36:23.072056, took: 0:01:00.129232
Warning: cannot update html pages for r-bioc-ensembldb
All cleanup done.
Wed 7 Dec 13:36:23 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-dhZzbzLP, which will now be removed.
Build step 'Execute shell' marked build as failure
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