[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_5 #63704
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Wed Dec 7 13:35:27 UTC 2016
https://jenkins.debian.net/job/reproducible_builder_amd64_5/63704/------------------------------------------
[...truncated 5782 lines...]
Setting up libxft2:amd64 (2.3.2-1) ...
Setting up fontconfig (2.11.0-6.7) ...
Regenerating fonts cache... done.
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxext6:amd64 (2:1.3.3-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libxss1:amd64 (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:amd64 (1.15~beta1-1) ...
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-base-dev (3.3.2-1) ...
Setting up r-cran-curl (2.3-1) ...
Setting up r-bioc-biocgenerics (0.20.0-1) ...
Setting up r-bioc-biobase (2.34.0-1) ...
Setting up r-cran-jsonlite (1.1-2) ...
Setting up r-cran-sourcetools (0.1.5-1) ...
Setting up r-bioc-biocinstaller (1.24.0-1) ...
Setting up r-cran-dbi (0.5-1-1) ...
Setting up r-cran-pkgkitten (0.1.4-1) ...
Setting up r-cran-rcpp (0.12.8-1) ...
Setting up r-cran-r6 (2.2.0-1) ...
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-bioc-s4vectors (0.12.0-1) ...
Setting up r-cran-httpuv (1.3.3-3) ...
Setting up r-cran-openssl (0.9.5-1) ...
Setting up r-cran-htmltools (0.3.5-2) ...
Setting up r-cran-shiny (0.14.2+dfsg-1) ...
Setting up r-cran-httr (1.2.1-1) ...
Setting up r-bioc-iranges (2.8.0-1) ...
Setting up r-bioc-interactivedisplaybase (1.12.0-1) ...
Setting up r-bioc-annotationdbi (1.36.0-1) ...
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-annotationhub
dpkg-buildpackage: info: source version 2.6.4-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-bioc-annotationhub-2.6.4
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: AnnotationHub Version: 2.6.4
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 10:43:21 +0100
mkdir -p /build/r-bioc-annotationhub-2.6.4/debian/r-bioc-annotationhub/usr/lib/R/site-library
R CMD INSTALL -l /build/r-bioc-annotationhub-2.6.4/debian/r-bioc-annotationhub/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 30 Nov 2016 10:43:21 +0100'"
* installing *source* package 'AnnotationHub' ...
** R
** inst
** preparing package for lazy loading
Warning in read.dcf(con) : unable to resolve 'bioconductor.org'
** 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 (AnnotationHub)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.10)
I: Using r-bioc-iranges for Suggests:IRanges
I: Using r-bioc-genomicranges for Suggests:GenomicRanges
I: Using r-bioc-genomeinfodb for Suggests:GenomeInfoDb
I: Using r-bioc-variantannotation for Suggests:VariantAnnotation
I: Using r-bioc-rsamtools for Suggests:Rsamtools
I: Using r-bioc-rtracklayer for Suggests:rtracklayer
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:AnnotationForge
W: Cannot find a debian package for Suggests:rBiopaxParser
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:MSnbase
W: Cannot find a debian package for Suggests:mzR
I: Using r-bioc-biostrings for Suggests:Biostrings
I: Using r-bioc-summarizedexperiment for Suggests:SummarizedExperiment
I: Using r-cran-rsqlite for Imports:RSQLite
I: Using r-bioc-biocinstaller for Imports:BiocInstaller
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-interactivedisplaybase for Imports:interactiveDisplayBase
I: Using r-cran-httr for Imports:httr
I: Using r-cran-yaml for Imports:yaml
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_installdeb -O--buildsystem=R
dh_gencontrol -O--buildsystem=R
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-annotationhub' in '../r-bioc-annotationhub_2.6.4-1_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-annotationhub_2.6.4-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-annotationhub-2.6.4
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/52596 and its subdirectories
I: Current time: Wed Dec 7 01:33:25 -12 2016
I: pbuilder-time-stamp: 1481117605
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),
247c247
< r-cran-curl (= 2.3-1),
---
> r-cran-curl (= 2.2-1),
253c253
< r-cran-jsonlite (= 1.1-2),
---
> r-cran-jsonlite (= 1.1-1),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-Jq77rSHC/tmp.rd7kqc6kzB: 81.8% -- replaced with /srv/reproducible-results/rbuild-debian-Jq77rSHC/tmp.rd7kqc6kzB.gz
INFO: Starting at 2016-12-07 13:34:26.712823
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-annotationhub'
CRITICAL: AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-07 13:35:26.849936, took: 0:01:00.137150
Warning: cannot update html pages for r-bioc-annotationhub
All cleanup done.
Wed 7 Dec 13:35:26 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-0rolTQED, which will now be removed.
Build step 'Execute shell' marked build as failure
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