[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_18 #4484

jenkins at jenkins.debian.net jenkins at jenkins.debian.net
Wed Dec 7 13:35:28 UTC 2016


https://jenkins.debian.net/job/reproducible_builder_amd64_18/4484/------------------------------------------
[...truncated 5041 lines...]
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-base-dev (3.3.2-1) ...
Setting up r-cran-lattice (0.20-34-1) ...
Setting up r-cran-foreign (0.8.67-1) ...
Setting up r-cran-sp (1:1.2-3-1) ...
Setting up dh-autoreconf (12) ...
Setting up debhelper (10.2.2) ...
Setting up dh-r (20160916) ...
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-cran-maptools
dpkg-buildpackage: info: source version 1:0.8-40+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille at debian.org>
 dpkg-source --before-build r-cran-maptools-0.8-40+dfsg
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: maptools Version: 0.8-40
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 09:08:03 +0100
	mkdir -p /build/r-cran-maptools-0.8-40\+dfsg/debian/r-cran-maptools/usr/lib/R/site-library
	R CMD INSTALL -l /build/r-cran-maptools-0.8-40\+dfsg/debian/r-cran-maptools/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 30 Nov 2016 09:08:03 +0100'"
* installing *source* package 'maptools' ...
files 'data/gpcholes.rda', 'data/state.vbm.rda', 'data/wrld_simpl.rda', 'inst/shapes/baltim.dbf', 'inst/shapes/baltim.shp', 'inst/shapes/baltim.shx', 'inst/shapes/columbus.dbf', 'inst/shapes/columbus.shp', 'inst/shapes/columbus.shx', 'inst/shapes/pointZ.dbf', 'inst/shapes/pointZ.prj', 'inst/shapes/pointZ.shp', 'inst/shapes/pointZ.shx', 'inst/shapes/sids.dbf', 'inst/shapes/sids.shp', 'inst/shapes/sids.shx' are missing
** libs
make[1]: Entering directory '/build/r-cran-maptools-0.8-40+dfsg/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rcentroid.c -o Rcentroid.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rgshhs.c -o Rgshhs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rshapeget.c -o Rshapeget.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rshapeinfo.c -o Rshapeinfo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rshapewrite.c -o Rshapewrite.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 Rshapewrite1.c -o Rshapewrite1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 insiders.c -o insiders.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 pip.c -o pip.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 shpopen.c -o shpopen.o
shpopen.c: In function 'SHPOpen':
shpopen.c:507:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( pabyBuf, 100, 1, psSHP->fpSHP );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -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 shptree.c -o shptree.o
shptree.c: In function 'SHPSearchDiskTree':
shptree.c:829:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( abyBuf, 16, 1, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c: In function 'SHPSearchDiskTreeNode':
shptree.c:731:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &offset, 4, 1, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c:734:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( adfNodeBoundsMin, sizeof(double), 2, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c:735:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( adfNodeBoundsMax, sizeof(double), 2, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c:744:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &numshapes, 4, 1, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c:771:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( *ppanResultBuffer + *pnResultCount,
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                sizeof(int), (size_t) numshapes, fp );
                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
shptree.c:786:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &numsubnodes, 4, 1, fp );
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o maptools.so Rcentroid.o Rgshhs.o Rshapeget.o Rshapeinfo.o Rshapewrite.o Rshapewrite1.o insiders.o pip.o shpopen.o shptree.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/build/r-cran-maptools-0.8-40+dfsg/src'
make[1]: Entering directory '/build/r-cran-maptools-0.8-40+dfsg/src'
make[1]: Leaving directory '/build/r-cran-maptools-0.8-40+dfsg/src'
installing to /build/r-cran-maptools-0.8-40+dfsg/debian/r-cran-maptools/usr/lib/R/site-library/maptools/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (maptools)
W: Ignoring specified R dependency: R (>= 2.10)
I: Using r-cran-sp for Depends:sp (>= 1.0-11)
W: Cannot find a debian package for Suggests:rgeos (>= 0.1-8)
I: Using r-cran-spatstat for Suggests:spatstat (>= 1.18)
W: Cannot find a debian package for Suggests:PBSmapping
I: Using r-cran-maps for Suggests:maps
I: Using r-cran-rcolorbrewer for Suggests:RColorBrewer
I: Using r-cran-raster for Suggests:raster
I: Using r-cran-polyclip for Suggests:polyclip
I: Using r-cran-foreign for Imports:foreign (>= 0.8)
I: Using r-cran-lattice for Imports:lattice
   debian/rules override_dh_install
make[1]: Entering directory '/build/r-cran-maptools-0.8-40+dfsg'
dh_install
find debian -name LICENSE -delete
make[1]: Leaving directory '/build/r-cran-maptools-0.8-40+dfsg'
   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-cran-maptools-dbgsym' in '../r-cran-maptools-dbgsym_0.8-40+dfsg-1_amd64.deb'.
dpkg-deb: building package 'r-cran-maptools' in '../r-cran-maptools_0.8-40+dfsg-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-cran-maptools_0.8-40+dfsg-1_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build r-cran-maptools-0.8-40+dfsg
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/31346 and its subdirectories
I: Current time: Tue Jan  9 07:55:40 -12 2018
I: pbuilder-time-stamp: 1515527740
9c9
<  binutils (= 2.27.51.20161127-1),
---
>  binutils (= 2.27.51.20161201-1),
25c25
<  dh-r (= 20160916),
---
>  dh-r (= 20161130),
175c175
<  libsystemd0 (= 232-6),
---
>  libsystemd0 (= 232-7),
188c188
<  libudev1 (= 232-6),
---
>  libudev1 (= 232-7),
Error: database is locked
Starting cleanup.
/srv/reproducible-results/rbuild-debian-owyenEev/tmp.vqknflLoEQ:	 81.2% -- replaced with /srv/reproducible-results/rbuild-debian-owyenEev/tmp.vqknflLoEQ.gz
INFO: Starting at 2016-12-07 13:34:27.856338
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-cran-maptools'
CRITICAL:                        AND s.architecture='amd64' AND s.suite='testing'"
CRITICAL: Exiting script.
INFO: Finished at 2016-12-07 13:35:27.984139, took: 0:01:00.127824








Warning: cannot update html pages for r-cran-maptools
All cleanup done.
Wed  7 Dec 13:35:28 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-YGnXPRPo, which will now be removed.
Build step 'Execute shell' marked build as failure



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