[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_delta #29935
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sun Aug 30 23:38:57 UTC 2015
See <https://jenkins.debian.net/job/reproducible_builder_delta/29935/>
------------------------------------------
[...truncated 1612 lines...]
Setting up liblapack3 (3.5.0-4) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-4) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:amd64 (5.1.1alpha+20120614-2.1) ...
Setting up libtinfo-dev:amd64 (6.0+20150810-1) ...
Setting up libncurses5-dev:amd64 (6.0+20150810-1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre16-3:amd64 (2:8.35-7.1) ...
Setting up libpcre32-3:amd64 (2:8.35-7.1) ...
Setting up libpcre3-dev:amd64 (2:8.35-7.1) ...
Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-2+b1) ...
Setting up libpng12-dev:amd64 (1.2.50-2+b2) ...
Setting up libreadline6-dev:amd64 (6.3-8+b3) ...
Setting up libreadline-dev:amd64 (6.3-8+b3) ...
Setting up libtcl8.6:amd64 (8.6.4+dfsg-2) ...
Setting up libtiff5:amd64 (4.0.3-13) ...
Setting up libtk8.6:amd64 (8.6.4+dfsg-2) ...
Setting up zip (3.0-11) ...
Setting up unzip (6.0-18) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.4) ...
Setting up r-base-core (3.2.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.2.2-1) ...
Setting up r-bioc-biocgenerics (0.14.0-1) ...
Processing triggers for libc-bin (2.19-19) ...
Processing triggers for systemd (224-2) ...
Processing triggers for ca-certificates (20150426) ...
Updating certificates in /etc/ssl/certs...
180 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...
disorderfs is already the newest version.
fakeroot is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying source file
I: copying [r-bioc-biobase_2.28.0-1.dsc]
I: copying [./r-bioc-biobase_2.28.0.orig.tar.gz]
I: copying [./r-bioc-biobase_2.28.0-1.debian.tar.xz]
I: Extracting source
gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made sam 09 mai 2015 20:50:40 GMT-14 using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-biobase_2.28.0-1.dsc
dpkg-source: info: extracting r-bioc-biobase in r-bioc-biobase-2.28.0
dpkg-source: info: unpacking r-bioc-biobase_2.28.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-biobase_2.28.0-1.debian.tar.xz
dpkg-source: info: applying exclude_testing_golubEsets.patch
I: Building the package
W: no hooks of type A found -- ignoring
I: Running cd tmp/buildd/*/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" dpkg-buildpackage -us -uc -b -rfakeroot
dpkg-buildpackage: source package r-bioc-biobase
dpkg-buildpackage: source version 2.28.0-1
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Andreas Tille <tille at debian.org>
dpkg-source --before-build r-bioc-biobase-2.28.0
dpkg-buildpackage: host architecture amd64
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
debian/rules build
test -x debian/rules
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:110: CDBS WARNING: DEB_DH_BUILDDEB_ARGS is deprecated since 0.4.85
fakeroot debian/rules binary
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
/usr/share/cdbs/1/rules/buildcore.mk:110: CDBS WARNING: DEB_DH_BUILDDEB_ARGS is deprecated since 0.4.85
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.2.2-1), r-api-3" >> debian/r-bioc-biobase.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library --clean \
. \
"--built-timestamp=\"Sat, 09 May 2015 08:46:24 +0200\"" \
; \
else \
R CMD INSTALL -l /tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library \
--clean . \
"--built-timestamp=\"Sat, 09 May 2015 08:46:24 +0200\"" \
; \
fi
* installing *source* package ‘Biobase’ ...
** libs
make[1]: Entering directory '/tmp/buildd/r-bioc-biobase-2.28.0/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c Rinit.c -o Rinit.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c anyMissing.c -o anyMissing.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c envir.c -o envir.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c matchpt.c -o matchpt.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rowMedians.c -o rowMedians.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c sublist_extract.c -o sublist_extract.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/tmp/buildd/r-bioc-biobase-2.28.0/src'
make[1]: Entering directory '/tmp/buildd/r-bioc-biobase-2.28.0/src'
make[1]: Leaving directory '/tmp/buildd/r-bioc-biobase-2.28.0/src'
installing to /tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/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 (Biobase)
rm -vf /tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library/R.css \
/tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/COPYING \
/tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/lib/R/site-library/Biobase/LICENSE.txt
if test -f debian/overrides; then \
install -d /tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/tmp/buildd/r-bioc-biobase-2.28.0/debian/r-bioc-biobase/usr/share/lintian/overrides/r-bioc-biobase; \
fi
Adding cdbs dependencies to debian/r-bioc-biobase.substvars
dh_installdirs -pr-bioc-biobase
echo "R:Depends=r-base-core (>= 3.2.2~)" >> debian/r-bioc-biobase.substvars
dh_installdocs -pr-bioc-biobase ./NEWS
dh_installexamples -pr-bioc-biobase
dh_installman -pr-bioc-biobase
dh_installinfo -pr-bioc-biobase
dh_installmenu -pr-bioc-biobase
dh_installcron -pr-bioc-biobase
dh_installinit -pr-bioc-biobase
dh_installdebconf -pr-bioc-biobase
dh_installemacsen -pr-bioc-biobase
dh_installcatalogs -pr-bioc-biobase
dh_installpam -pr-bioc-biobase
dh_installlogrotate -pr-bioc-biobase
dh_installlogcheck -pr-bioc-biobase
dh_installchangelogs -pr-bioc-biobase
dh_installudev -pr-bioc-biobase
dh_lintian -pr-bioc-biobase
dh_bugfiles -pr-bioc-biobase
dh_install -pr-bioc-biobase
dh_link -pr-bioc-biobase
dh_installmime -pr-bioc-biobase
dh_installgsettings -pr-bioc-biobase
dh_strip -pr-bioc-biobase
dh_strip_nondeterminism
dh_compress -pr-bioc-biobase
dh_fixperms -pr-bioc-biobase
dh_makeshlibs -pr-bioc-biobase
dh_installdeb -pr-bioc-biobase
dh_perl -pr-bioc-biobase
dh_shlibdeps -pr-bioc-biobase
dh_gencontrol -pr-bioc-biobase
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 -pr-bioc-biobase
dh_builddeb -pr-bioc-biobase -- -Z xz
dpkg-deb: building package 'r-bioc-biobase-dbgsym' in '../r-bioc-biobase-dbgsym_2.28.0-1_amd64.deb'.
dpkg-deb: building package 'r-bioc-biobase' in '../r-bioc-biobase_2.28.0-1_amd64.deb'.
dpkg-genbuildinfo >../r-bioc-biobase_2.28.0-1_amd64.buildinfo
dpkg-distaddfile r-bioc-biobase_2.28.0-1_amd64.buildinfo gnu-r optional
dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges -b >../r-bioc-biobase_2.28.0-1_amd64.changes
dpkg-genchanges: warning: package r-bioc-biobase-dbgsym listed in files list but not in control info
dpkg-genchanges: binary-only upload (no source code included)
dpkg-source --after-build r-bioc-biobase-2.28.0
dpkg-buildpackage: binary-only upload (no source included)
I: user script /var/cache/pbuilder/build//28971/tmp/hooks/B01_cleanup starting
I: user script /var/cache/pbuilder/build//28971/tmp/hooks/B01_cleanup finished
I: unmounting /sys filesystem
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: cleaning the build env
I: removing directory /var/cache/pbuilder/build//28971 and its subdirectories
I: Current time: lundi 31 août 2015, 13:38:57 (UTC+1400)
I: pbuilder-time-stamp: 1440977937
+ true
+ '[' -f b2/r-bioc-biobase_2.28.0-1_amd64.changes ']'
+ FTBFS=0
+ cat b1/r-bioc-biobase_2.28.0-1_amd64.changes
+ tee -a /srv/reproducible-results/tmp.Ua9RvR3hs3/tmp.EVmI0G05o7
Format: 1.8
Date: Sat, 09 May 2015 08:46:24 +0200
Source: r-bioc-biobase
Binary: r-bioc-biobase
Architecture: amd64
Version: 2.28.0-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Andreas Tille <tille at debian.org>
Description:
r-bioc-biobase - base functions for Bioconductor
Changes:
r-bioc-biobase (2.28.0-1) unstable; urgency=medium
.
* New upstream version
Checksums-Sha1:
ffca0df7aa93676ab91ae8b79ee349095eb83149 16834 r-bioc-biobase-dbgsym_2.28.0-1_amd64.deb
360ca5e25d1eb4eb35ab1c2b956edb1831dd260a 7509 r-bioc-biobase_2.28.0-1_amd64.buildinfo
3518f0a191edf3f60b894a76e7f4aaac1f6ba1d2 1996876 r-bioc-biobase_2.28.0-1_amd64.deb
Checksums-Sha256:
dd542c85d3f0b0ead172e58860523bdc376069c5dc31d033e285c76706a4922f 16834 r-bioc-biobase-dbgsym_2.28.0-1_amd64.deb
13958ecb455766482a77f43b4bf504595805425429d3e7aa48271b082d058513 7509 r-bioc-biobase_2.28.0-1_amd64.buildinfo
06eccbda108db66a8af1b9f656899f1a3c25f7fe48aadbe323b38c16331cec3f 1996876 r-bioc-biobase_2.28.0-1_amd64.deb
Files:
f56bf656f383630fbc1c480462275c00 16834 debugsym extra r-bioc-biobase-dbgsym_2.28.0-1_amd64.deb
5473c3ea39902af704e234f446752663 7509 gnu-r optional r-bioc-biobase_2.28.0-1_amd64.buildinfo
125a1d16664dea30e77eeca56f03578d 1996876 gnu-r optional r-bioc-biobase_2.28.0-1_amd64.deb
+ rm
rm: missing operand
Try 'rm --help' for more information.
+ cleanup_all
+ '[' 0 -eq 1 ']'
+ '[' '' = failure ']'
+ '[' '!' -z '' ']'
+ gzip -9fvn /srv/reproducible-results/tmp.Ua9RvR3hs3/tmp.EVmI0G05o7
/srv/reproducible-results/tmp.Ua9RvR3hs3/tmp.EVmI0G05o7: 78.1% -- replaced with /srv/reproducible-results/tmp.Ua9RvR3hs3/tmp.EVmI0G05o7.gz
+ '[' legacy = legacy ']'
+ gen_package_html r-bioc-biobase
+ cd /srv/jenkins/bin
+ python3 -c 'import reproducible_html_packages as rep
pkg = rep.Package('\''r-bioc-biobase'\'', no_notes=True)
rep.gen_packages_html([pkg], no_clean=True)'
INFO: Starting at 2015-08-30 23:38:57.801772
INFO: Finished at 2015-08-30 23:38:57.815598, took: 0:00:00.013845
+ cd -
+ cd
+ rm -r /srv/reproducible-results/tmp.Ua9RvR3hs3
+ false
+ rm -f /tmp/reproducible-lockfile-unstable-amd64-r-bioc-biobase
Sun 30 Aug 23:38:57 UTC 2015 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-P5HKDNPw, which will now be removed.
Build step 'Execute shell' marked build as failure
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