[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_arm64_19 #1588
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Fri Jan 6 04:10:12 UTC 2017
https://jenkins.debian.net/job/reproducible_builder_arm64_19/1588/------------------------------------------
[...truncated 628.75 KB...]
Testing across_genes ... [[32mPASS[0m]
Testing across_genes ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
Testing across_intron ... [[32mPASS[0m]
../../bin/exactSNP -g ../chr901.fa -o result/test-out.VCF -i data/test-in.BAM -b
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
v1.5.1
//============================= exactSNP setting =============================\\
|| ||
|| Input file : data/test-in.BAM (BAM) ||
|| Output file : result/test-out.VCF ||
|| Reference genome : ../chr901.fa ||
|| ||
|| Threads : 1 ||
|| Min supporting reads : 1 ||
|| Min pct. of supporting reads : 0.0% ||
|| Min base quality score : 13 ||
|| Number of trimmed bases : 3 ||
|| ||
|| Q value cutoff : 10E-12.0 ||
|| P value upper bound : 0.00500 ||
|| Flanking windows size : 5 ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
//====================== Running (09-Feb-2018 00:31:28) ======================\\
|| ||
|| Split BAM file into ./temp-snps-004719-F28A804300BF-* ... ||
|| processed block chr901 at 999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
|| ||
\\============================================================================//
//================================= Summary ==================================\\
|| ||
|| Processed reads : 50204 ||
|| Reported SNPs : 415 ||
|| Reported indels : 21 ||
|| ||
|| Running time : 0.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
[30;47m
**************************************************
**************************************************
*** ***
*** Test finished. ***
*** ***
*** Should there be any error, please visit ***
*** [34mhttp://subread.sourceforge.net/[0;30;47m for more ***
*** information. ***
*** ***
**************************************************
**************************************************
[0m
make[1]: Leaving directory '/build/subread-1.5.1+dfsg/2nd'
fakeroot debian/rules binary
dh binary --parallel
dh_testroot
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/subread-1.5.1+dfsg/2nd'
find /build/subread-1.5.1+dfsg/2nd -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
mkdir -p /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1
help2man --no-info --help-option="''" --no-discard-stderr --name='an accurate and efficient aligner for mapping both genomic \
DNA-seq reads and RNA-seq reads (for the purpose of expression analysis)' \
/build/subread-1.5.1+dfsg/2nd/bin/subread-align | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/subread-align.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='builds an base-space or color-space index using the reference sequences' \
/build/subread-1.5.1+dfsg/2nd/bin/subread-buildindex | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/subread-buildindex.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='an RNA-seq aligner suitable for all purposes of RNA-seq analyses' \
/build/subread-1.5.1+dfsg/2nd/bin/subjunc | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/subjunc.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a highly efficient and accurate read summarization program' \
/build/subread-1.5.1+dfsg/2nd/bin/featureCounts | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/featureCounts.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='a SNP caller that discovers SNPs by testing signals against local background noises' \
/build/subread-1.5.1+dfsg/2nd/bin/exactSNP | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/exactSNP.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='detect short and long indels' \
/build/subread-1.5.1+dfsg/2nd/bin/subindel | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/subindel.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='scans the entire genome and reports all matches of a specified sequence' \
/build/subread-1.5.1+dfsg/2nd/bin/utilities/subread-fullscan | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/subread-fullscan.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='counting the coverage of mapped reads at each location on the entire reference genome' \
/build/subread-1.5.1+dfsg/2nd/bin/utilities/coverageCount | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/coverageCount.1;
help2man --no-info --help-option="''" --no-discard-stderr --name='calculate the proportion of mapped reads/fragments' \
/build/subread-1.5.1+dfsg/2nd/bin/utilities/propmapped | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/propmapped.1;
for i in removeDup repair qualityScores ; do \
help2man --no-info --help-option="''" --no-discard-stderr --name='a component of subread suite' /build/subread-1.5.1+dfsg/2nd/bin/utilities/$i | debian/filter.pl > /build/subread-1.5.1+dfsg/2nd/debian/subread/usr/share/man/man1/$i.1; \
done
dh_auto_install
make[1]: Leaving directory '/build/subread-1.5.1+dfsg/2nd'
dh_install
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installexamples-indep
make[1]: Entering directory '/build/subread-1.5.1+dfsg/2nd'
tar --sort=name \
--mtime="@1480663325" \
--owner=root --group=root --numeric-owner \
--mode=go=rX,u+rw,a-s \
-cJf /build/subread-1.5.1+dfsg/2nd/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/
make[1]: Leaving directory '/build/subread-1.5.1+dfsg/2nd'
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dpkg-shlibdeps: warning: tried to merge the same object (ld-linux-aarch64.so.1) twice in a symfile
dh_installdeb
dh_gencontrol
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
dpkg-gencontrol: warning: Depends field of package subread-data: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums
dh_builddeb
dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.5.1+dfsg-4_arm64.deb'.
dpkg-deb: building package 'subread-data' in '../subread-data_1.5.1+dfsg-4_all.deb'.
dpkg-deb: building package 'subread' in '../subread_1.5.1+dfsg-4_arm64.deb'.
dpkg-genbuildinfo --build=binary
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-genchanges --build=binary >../subread_1.5.1+dfsg-4_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build 2nd
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
I: user script /srv/workspace/pbuilder/12170/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/12170/tmp/hooks/B01_cleanup finished
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/12170 and its subdirectories
I: Current time: Fri Feb 9 00:33:05 +14 2018
I: pbuilder-time-stamp: 1518085985
+ PRESULT=0
+ set -e
+ '[' 0 -eq 124 ']'
+ false
Thu Feb 8 10:33:05 UTC 2018 I: Signing ./b2/subread_1.5.1+dfsg-4_arm64.buildinfo as subread_1.5.1+dfsg-4_arm64.buildinfo.asc
+ set +x
Thu Feb 8 10:33:05 UTC 2018 I: Signed ./b2/subread_1.5.1+dfsg-4_arm64.buildinfo as ./b2/subread_1.5.1+dfsg-4_arm64.buildinfo.asc
Thu Feb 8 10:33:05 UTC 2018 - build #2 for subread/unstable/arm64 on codethink-sled13-arm64 done.
Starting cleanup.
/srv/reproducible-results/rbuild-debian-dWqU3H0i/tmp.5cqrq0eTK1: 57.4% -- replaced with /srv/reproducible-results/rbuild-debian-dWqU3H0i/tmp.5cqrq0eTK1.gz
All cleanup done.
Thu Feb 8 10:33:05 UTC 2018 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-R0LBu15g, which will now be removed.
/srv/reproducible-results/rbuild-debian-1ZNKP3oK:
total 156
drwxr-xr-x 2 jenkins jenkins 4096 Jan 6 04:04 b1
drwxr-xr-x 2 jenkins jenkins 4096 Jan 6 04:10 b2
-rw-r--r-- 1 jenkins jenkins 2243 Dec 2 07:57 subread_1.5.1+dfsg-4.dsc
-rw------- 1 jenkins jenkins 140115 Jan 6 04:04 tmp.Pv4V9EWAOw
/srv/reproducible-results/rbuild-debian-1ZNKP3oK/b1:
total 24584
-rw-r--r-- 1 jenkins jenkins 136480 Jan 6 04:04 build.log
-rw-r--r-- 1 jenkins jenkins 18452468 Jan 6 04:04 subread-data_1.5.1+dfsg-4_all.deb
-rw-r--r-- 1 jenkins jenkins 6036098 Jan 6 04:04 subread-dbgsym_1.5.1+dfsg-4_arm64.deb
-rw-r--r-- 1 jenkins jenkins 5061 Jan 6 04:04 subread_1.5.1+dfsg-4_arm64.buildinfo
-rw-r--r-- 1 jenkins jenkins 5927 Jan 6 04:04 subread_1.5.1+dfsg-4_arm64.buildinfo.asc
-rw-r--r-- 1 jenkins jenkins 1762 Jan 6 04:04 subread_1.5.1+dfsg-4_arm64.changes
-rw-r--r-- 1 jenkins jenkins 476024 Jan 6 04:04 subread_1.5.1+dfsg-4_arm64.deb
/srv/reproducible-results/rbuild-debian-1ZNKP3oK/b2:
total 24808
-rw-r--r-- 1 jenkins jenkins 366298 Jan 6 04:10 build.log
-rw-r--r-- 1 jenkins jenkins 18452468 Jan 6 04:10 subread-data_1.5.1+dfsg-4_all.deb
-rw-r--r-- 1 jenkins jenkins 6036098 Jan 6 04:10 subread-dbgsym_1.5.1+dfsg-4_arm64.deb
-rw-r--r-- 1 jenkins jenkins 5061 Jan 6 04:10 subread_1.5.1+dfsg-4_arm64.buildinfo
-rw-r--r-- 1 jenkins jenkins 5927 Jan 6 04:10 subread_1.5.1+dfsg-4_arm64.buildinfo.asc
-rw-r--r-- 1 jenkins jenkins 1762 Jan 6 04:10 subread_1.5.1+dfsg-4_arm64.changes
-rw-r--r-- 1 jenkins jenkins 476024 Jan 6 04:10 subread_1.5.1+dfsg-4_arm64.deb
Fri Jan 6 04:10:10 UTC 2017 I: subread_1.5.1+dfsg-4_arm64.changes:
Format: 1.8
Date: Fri, 02 Dec 2016 08:22:05 +0100
Source: subread
Binary: subread subread-data
Architecture: all arm64
Version: 1.5.1+dfsg-4
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:
subread - toolkit for processing next-gen sequencing data
subread-data - data files for subread package
Changes:
subread (1.5.1+dfsg-4) unstable; urgency=medium
.
* Fix watch file
* debhelper 10
* remove outdated information from README.source
Checksums-Sha1:
36d087a736a602281410cba832bfc7cec3ba7090 18452468 subread-data_1.5.1+dfsg-4_all.deb
867046f56537560b5bf0a2aa65a3333f46b1ab57 6036098 subread-dbgsym_1.5.1+dfsg-4_arm64.deb
a569484de445c0413f7d6927a1661fb00c28b258 5061 subread_1.5.1+dfsg-4_arm64.buildinfo
48ee1ecd5e527067bc27e7e136967c90e391e4cc 476024 subread_1.5.1+dfsg-4_arm64.deb
Checksums-Sha256:
58289e10adcb9a3a390dc1e98202ca50c680e4021b5985c3c69ee7a2ab781943 18452468 subread-data_1.5.1+dfsg-4_all.deb
44a8572d91d022d719cb13582ec4952774a0b5096f356c09500ff53eb1eb40fc 6036098 subread-dbgsym_1.5.1+dfsg-4_arm64.deb
a95273fcfe2051117a48b220f61224c581924e047cbd2c398c5220fabbea118d 5061 subread_1.5.1+dfsg-4_arm64.buildinfo
59e65208670deecf4daae3e0d8203c0ba488050ed97ede3e3c5b9608749e7b88 476024 subread_1.5.1+dfsg-4_arm64.deb
Files:
3bee54657f43e02725e9b22354e5a8c3 18452468 science optional subread-data_1.5.1+dfsg-4_all.deb
afd62edfcf925d16d1e9a2a9c9798bfa 6036098 debug extra subread-dbgsym_1.5.1+dfsg-4_arm64.deb
85505ab1a98b37029c15e4cdc85631e9 5061 science optional subread_1.5.1+dfsg-4_arm64.buildinfo
f4877cf7cf9f998fec5f8f5dd6d5bf1a 476024 science optional subread_1.5.1+dfsg-4_arm64.deb
Diff of the two buildlogs:
--
tee: /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/subread_1.5.1+dfsg-4.diff: No space left on device
Starting cleanup.
/srv/reproducible-results/rbuild-debian-1ZNKP3oK/tmp.Pv4V9EWAOw: 87.0% -- replaced with /srv/reproducible-results/rbuild-debian-1ZNKP3oK/tmp.Pv4V9EWAOw.gz
INFO: Starting at 2017-01-06 04:10:11.777782
CRITICAL: buildinfo not detected at /var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/i386/subread_1.5.1+dfsg-4_i386.buildinfo
CRITICAL: https://tests.reproducible-builds.org/debian/unstable/i386/subread didn't produce a buildlog, even though it has been built.
INFO: Finished at 2017-01-06 04:10:12.074805, took: 0:00:00.297042
All cleanup done.
Fri 6 Jan 04:10:12 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-VtUjXhCU, which will now be removed.
Build step 'Execute shell' marked build as failure
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