[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_31 #3474

jenkins at jenkins.debian.net jenkins at jenkins.debian.net
Wed Dec 7 13:37:15 UTC 2016


https://jenkins.debian.net/job/reproducible_builder_amd64_31/3474/------------------------------------------
[...truncated 7245 lines...]
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-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-summarizedexperiment (1.4.0-1) ...
Setting up r-bioc-biomart (2.30.0-1) ...
Setting up r-cran-rpart (4.1-10-2) ...
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-cran-hmisc (3.17-4-2) ...
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 r-bioc-ensembldb (1.6.2-1) ...
Setting up r-bioc-variantannotation (1.20.1-1) ...
Setting up r-bioc-biovizbase (1.22.0-1) ...
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-gviz
dpkg-buildpackage: info: source version 1.18.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build r-bioc-gviz-1.18.1
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: Gviz Version: 1.18.1
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 11:06:08 +0100
	mkdir -p /build/r-bioc-gviz-1.18.1/debian/r-bioc-gviz/usr/lib/R/site-library
	R CMD INSTALL -l /build/r-bioc-gviz-1.18.1/debian/r-bioc-gviz/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 30 Nov 2016 11:06:08 +0100'"
* installing *source* package 'Gviz' ...
** R
** data
** 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 (Gviz)
W: Ignoring specified R dependency: R (>= 2.10.0)
I: Using r-bioc-s4vectors for Depends:S4Vectors (>= 0.9.25)
I: Using r-bioc-iranges for Depends:IRanges (>= 1.99.18)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.17.20)
I: Using r-cran-xtable for Suggests:xtable
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-xvector for Imports:XVector (>= 0.5.7)
I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.25.13)
I: Using r-cran-lattice for Imports:lattice
I: Using r-cran-rcolorbrewer for Imports:RColorBrewer
I: Using r-bioc-biomart for Imports:biomaRt (>= 2.11.0)
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.27.5)
I: Using r-bioc-biobase for Imports:Biobase (>= 2.15.3)
I: Using r-bioc-genomicfeatures for Imports:GenomicFeatures (>= 1.17.22)
I: Using r-bioc-bsgenome for Imports:BSgenome (>= 1.33.1)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.33.11)
I: Using r-bioc-biovizbase for Imports:biovizBase (>= 1.13.8)
I: Using r-bioc-rsamtools for Imports:Rsamtools (>= 1.17.28)
I: Using r-cran-latticeextra for Imports:latticeExtra (>= 0.6-26)
I: Using r-cran-matrixstats for Imports:matrixStats (>= 0.8.14)
I: Using r-bioc-genomicalignments for Imports:GenomicAlignments (>= 1.1.16)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.11.3)
I: Using r-cran-digest for Imports:digest (>= 0.6.8)
   debian/rules override_dh_install
make[1]: Entering directory '/build/r-bioc-gviz-1.18.1'
dh_install
find debian -name "*.R" -exec chmod -x \{\} \;
make[1]: Leaving directory '/build/r-bioc-gviz-1.18.1'
   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
dpkg-gencontrol: warning: package r-bioc-gviz: unused substitution variable ${perl:Depends}
   dh_md5sums -O--buildsystem=R
   dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-bioc-gviz' in '../r-bioc-gviz_1.18.1-1_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-gviz_1.18.1-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build r-bioc-gviz-1.18.1
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/59680 and its subdirectories
I: Current time: Wed Dec  7 01:35:13 -12 2016
I: pbuilder-time-stamp: 1481117713
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),
250,251c249,250
<  r-bioc-ensembldb (= 1.6.2-1),
<  r-bioc-genomeinfodb (= 1.10.1-1),
---
>  r-bioc-ensembldb (= 1.6.0-1),
>  r-bioc-genomeinfodb (= 1.10.0-1),
261c260
<  r-bioc-variantannotation (= 1.20.1-1),
---
>  r-bioc-variantannotation (= 1.20.0-1),
268,269c267,268
<  r-cran-colorspace (= 1.3-1-1),
<  r-cran-curl (= 2.3-1),
---
>  r-cran-colorspace (= 1.2-7-1),
>  r-cran-curl (= 2.2-1),
285c284
<  r-cran-jsonlite (= 1.1-2),
---
>  r-cran-jsonlite (= 1.1-1),
319d317
<  r-cran-yaml (= 2.1.13-5),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-JZPl1Ujh/tmp.LP1jeLGEoQ:	 82.0% -- replaced with /srv/reproducible-results/rbuild-debian-JZPl1Ujh/tmp.LP1jeLGEoQ.gz
INFO: Starting at 2016-12-07 13:36:15.036678
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-gviz'
CRITICAL:                        AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-07 13:37:15.158252, took: 0:01:00.121606








Warning: cannot update html pages for r-bioc-gviz
All cleanup done.
Wed  7 Dec 13:37:15 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-o5HkUrgr, which will now be removed.
Build step 'Execute shell' marked build as failure



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