[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_i386_11 #29048
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Fri Jan 6 04:06:16 UTC 2017
https://jenkins.debian.net/job/reproducible_builder_i386_11/29048/------------------------------------------
[...truncated 495.33 KB...]
+|| 33%, 0 mins elapsed, rate=1926.4k bps/s, total=0m ||
+|| 41%, 0 mins elapsed, rate=2072.6k bps/s, total=0m ||
+|| 49%, 0 mins elapsed, rate=2202.2k bps/s, total=0m ||
+|| 58%, 0 mins elapsed, rate=2305.2k bps/s, total=0m ||
+|| 66%, 0 mins elapsed, rate=2423.8k bps/s, total=0m ||
+|| 74%, 0 mins elapsed, rate=2524.8k bps/s, total=0m ||
+|| 83%, 0 mins elapsed, rate=2620.0k bps/s, total=0m ||
+|| 91%, 0 mins elapsed, rate=2727.6k bps/s, total=0m ||
+|| 99%, 0 mins elapsed, rate=2792.7k bps/s, total=0m ||
|| 2 uninformative subreads were found. ||
|| These subreads were excluded from index building. ||
|| Build the index... ||
-|| 8%, 0 mins elapsed, rate=300.8k bps/s, total=0m ||
-|| 16%, 0 mins elapsed, rate=242.2k bps/s, total=0m ||
-|| 24%, 0 mins elapsed, rate=232.5k bps/s, total=0m ||
-|| 33%, 0 mins elapsed, rate=233.4k bps/s, total=0m ||
-|| 41%, 0 mins elapsed, rate=238.6k bps/s, total=0m ||
-|| 49%, 0 mins elapsed, rate=248.8k bps/s, total=0m ||
-|| 58%, 0 mins elapsed, rate=262.2k bps/s, total=0m ||
-|| 66%, 0 mins elapsed, rate=284.6k bps/s, total=0m ||
-|| 74%, 0 mins elapsed, rate=294.4k bps/s, total=0m ||
-|| 83%, 0 mins elapsed, rate=303.4k bps/s, total=0m ||
-|| 91%, 0 mins elapsed, rate=307.6k bps/s, total=0m ||
-|| 99%, 0 mins elapsed, rate=313.6k bps/s, total=0m ||
+|| 8%, 0 mins elapsed, rate=1003.8k bps/s, total=0m ||
+|| 16%, 0 mins elapsed, rate=1048.0k bps/s, total=0m ||
+|| 24%, 0 mins elapsed, rate=1131.0k bps/s, total=0m ||
+|| 33%, 0 mins elapsed, rate=1207.5k bps/s, total=0m ||
+|| 41%, 0 mins elapsed, rate=1281.8k bps/s, total=0m ||
+|| 49%, 0 mins elapsed, rate=1358.4k bps/s, total=0m ||
+|| 58%, 0 mins elapsed, rate=1436.5k bps/s, total=0m ||
+|| 66%, 0 mins elapsed, rate=1518.3k bps/s, total=0m ||
+|| 74%, 0 mins elapsed, rate=1602.3k bps/s, total=0m ||
+|| 83%, 0 mins elapsed, rate=1683.2k bps/s, total=0m ||
+|| 91%, 0 mins elapsed, rate=1776.1k bps/s, total=0m ||
+|| 99%, 0 mins elapsed, rate=1854.9k bps/s, total=0m ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
@@ -1406,7 +1423,7 @@
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
-|| Total running time: 0.1 minutes. ||
+|| Total running time: 0.0 minutes. ||
|| Index ../small1 was successfully built! ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
@@ -1442,18 +1459,18 @@
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
-//====================== Running (05-Jan-2017 15:59:59) ======================\\
+//====================== Running (09-Feb-2018 00:28:15) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
-|| 41% completed, 0.1 mins elapsed, rate=5.9k fragments per second ||
-|| 48% completed, 0.1 mins elapsed, rate=5.8k fragments per second ||
-|| 54% completed, 0.1 mins elapsed, rate=5.8k fragments per second ||
-|| 61% completed, 0.1 mins elapsed, rate=5.9k fragments per second ||
-|| 77% completed, 0.1 mins elapsed, rate=1.7k fragments per second ||
-|| 87% completed, 0.1 mins elapsed, rate=1.9k fragments per second ||
-|| 97% completed, 0.1 mins elapsed, rate=2.1k fragments per second ||
+|| 41% completed, 0.0 mins elapsed, rate=15.7k fragments per second ||
+|| 48% completed, 0.0 mins elapsed, rate=15.7k fragments per second ||
+|| 54% completed, 0.0 mins elapsed, rate=15.8k fragments per second ||
+|| 61% completed, 0.0 mins elapsed, rate=15.8k fragments per second ||
+|| 77% completed, 0.0 mins elapsed, rate=5.3k fragments per second ||
+|| 87% completed, 0.0 mins elapsed, rate=5.7k fragments per second ||
+|| 97% completed, 0.0 mins elapsed, rate=6.1k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -1467,7 +1484,7 @@
|| Junctions : 425 ||
|| Indels : 187 ||
|| ||
-|| Running time : 0.2 minutes ||
+|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
@@ -1502,18 +1519,18 @@
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
-//====================== Running (05-Jan-2017 16:00:08) ======================\\
+//====================== Running (09-Feb-2018 00:28:18) ======================\\
|| ||
|| The input file contains base space reads. ||
|| The range of Phred scores observed in the data is [2,41] ||
|| Load the 1-th index block... ||
-|| 41% completed, 0.1 mins elapsed, rate=2.7k fragments per second ||
-|| 48% completed, 0.1 mins elapsed, rate=2.7k fragments per second ||
-|| 54% completed, 0.1 mins elapsed, rate=2.8k fragments per second ||
-|| 61% completed, 0.2 mins elapsed, rate=2.8k fragments per second ||
-|| 77% completed, 0.2 mins elapsed, rate=1.2k fragments per second ||
-|| 87% completed, 0.2 mins elapsed, rate=1.3k fragments per second ||
-|| 97% completed, 0.2 mins elapsed, rate=1.3k fragments per second ||
+|| 41% completed, 0.0 mins elapsed, rate=8.9k fragments per second ||
+|| 48% completed, 0.0 mins elapsed, rate=9.0k fragments per second ||
+|| 54% completed, 0.0 mins elapsed, rate=9.0k fragments per second ||
+|| 61% completed, 0.0 mins elapsed, rate=9.0k fragments per second ||
+|| 77% completed, 0.0 mins elapsed, rate=4.1k fragments per second ||
+|| 87% completed, 0.1 mins elapsed, rate=4.4k fragments per second ||
+|| 97% completed, 0.1 mins elapsed, rate=4.6k fragments per second ||
|| ||
|| Completed successfully. ||
|| ||
@@ -1528,7 +1545,7 @@
|| Fusions : 99 ||
|| Indels : 188 ||
|| ||
-|| Running time : 0.2 minutes ||
+|| Running time : 0.1 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
@@ -1693,9 +1710,9 @@
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
-//====================== Running (05-Jan-2017 16:00:30) ======================\\
+//====================== Running (09-Feb-2018 00:28:23) ======================\\
|| ||
-|| Split BAM file into ./temp-snps-010703-15AD1E4A5976-* ... ||
+|| Split BAM file into ./temp-snps-065499-FB8C6E97A34D-* ... ||
|| processed block chr901 at 999950 by thread 1/1 [block number=1/1] ||
|| ||
|| Completed successfully. ||
@@ -1708,7 +1725,7 @@
|| Reported SNPs : 415 ||
|| Reported indels : 21 ||
|| ||
-|| Running time : 0.1 minutes ||
+|| Running time : 0.0 minutes ||
|| ||
\\===================== http://subread.sourceforge.net/ ======================//
@@ -1728,50 +1745,50 @@
[0m
-make[1]: Leaving directory '/build/1st/subread-1.5.1+dfsg'
+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/1st/subread-1.5.1+dfsg'
-find /build/1st/subread-1.5.1+dfsg -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${name%.*}"' \;
-mkdir -p /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1
+make[1]: Entering directory '/build/subread-1.5.1+dfsg/2nd'
+find /build/subread-1.5.1+dfsg/2nd -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "${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/1st/subread-1.5.1+dfsg/bin/subread-align | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-align.1;
+/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/1st/subread-1.5.1+dfsg/bin/subread-buildindex | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-buildindex.1;
+/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/1st/subread-1.5.1+dfsg/bin/subjunc | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subjunc.1;
+/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/1st/subread-1.5.1+dfsg/bin/featureCounts | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/featureCounts.1;
+/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/1st/subread-1.5.1+dfsg/bin/exactSNP | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/exactSNP.1;
+/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/1st/subread-1.5.1+dfsg/bin/subindel | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subindel.1;
+/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/1st/subread-1.5.1+dfsg/bin/utilities/subread-fullscan | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/subread-fullscan.1;
+/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/1st/subread-1.5.1+dfsg/bin/utilities/coverageCount | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/coverageCount.1;
+/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/1st/subread-1.5.1+dfsg/bin/utilities/propmapped | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/propmapped.1;
+/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/1st/subread-1.5.1+dfsg/bin/utilities/$i | debian/filter.pl > /build/1st/subread-1.5.1+dfsg/debian/subread/usr/share/man/man1/$i.1; \
+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/1st/subread-1.5.1+dfsg'
+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/1st/subread-1.5.1+dfsg'
+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/1st/subread-1.5.1+dfsg/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/
-make[1]: Leaving directory '/build/1st/subread-1.5.1+dfsg'
+ -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
@@ -1789,22 +1806,24 @@
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_i386.deb'.
dpkg-deb: building package 'subread-data' in '../subread-data_1.5.1+dfsg-4_all.deb'.
+dpkg-deb: building package 'subread-dbgsym' in '../subread-dbgsym_1.5.1+dfsg-4_i386.deb'.
dpkg-deb: building package 'subread' in '../subread_1.5.1+dfsg-4_i386.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_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
- dpkg-source --after-build subread-1.5.1+dfsg
+ dpkg-source --after-build 2nd
dpkg-buildpackage: info: binary-only upload (no source included)
I: copying local configuration
+I: user script /srv/workspace/pbuilder/15649/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/15649/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/31082 and its subdirectories
-I: Current time: Thu Jan 5 16:04:06 -12 2017
-I: pbuilder-time-stamp: 1483675446
+I: removing directory /srv/workspace/pbuilder/15649 and its subdirectories
+I: Current time: Fri Feb 9 00:29:07 +14 2018
+I: pbuilder-time-stamp: 1518085747
Starting cleanup.
/srv/reproducible-results/rbuild-debian-5rkMjz3D/tmp.Zw43BOUcTo: 86.9% -- replaced with /srv/reproducible-results/rbuild-debian-5rkMjz3D/tmp.Zw43BOUcTo.gz
INFO: Starting at 2017-01-06 04:06:16.043337
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 04:06:16.376588, took: 0:00:00.333262
All cleanup done.
Fri 6 Jan 04:06:16 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-00whW5MG, which will now be removed.
Build step 'Execute shell' marked build as failure
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