[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_arm64_6 #1306

jenkins at jenkins.debian.net jenkins at jenkins.debian.net
Sun Jan 8 07:48:20 UTC 2017 

https://jenkins.debian.net/job/reproducible_builder_arm64_6/1306/------------------------------------------
[...truncated 469.77 KB...]
    exercise   78 [             hmmpfam] ...     ok.
    exercise   79 [           hmmpfam/h] ...     ok.
    exercise   80 [           hmmpfam/n] ...     ok.
    exercise   81 [           hmmpfam/A] ...     ok.
    exercise   82 [           hmmpfam/E] ...     ok.
    exercise   83 [           hmmpfam/T] ...     ok.
    exercise   84 [           hmmpfam/Z] ...     ok.
    exercise   85 [         hmmpfam/acc] ...     ok.
    exercise   86 [      hmmpfam/compat] ...     ok.
    exercise   87 [      hmmpfam/cut_ga] ...     ok.
    exercise   88 [      hmmpfam/cut_nc] ...     ok.
    exercise   89 [      hmmpfam/cut_tc] ...     ok.
    exercise   90 [        hmmpfam/domE] ...     ok.
    exercise   91 [        hmmpfam/domT] ...     ok.
    exercise   92 [     hmmpfam/forward] ...     ok.
    exercise   93 [    hmmpfam/informat] ...     ok.
    exercise   94 [       hmmpfam/null2] ...     ok.
    exercise   95 [         hmmpfam/xnu] ...     ok.
    exercise   96 [           hmmsearch] ...     ok.
    exercise   97 [         hmmsearch/h] ...     ok.
    exercise   98 [         hmmsearch/A] ...     ok.
    exercise   99 [         hmmsearch/E] ...     ok.
    exercise  100 [         hmmsearch/T] ...     ok.
    exercise  101 [         hmmsearch/Z] ...     ok.
    exercise  102 [    hmmsearch/compat] ...     ok.
    exercise  103 [    hmmsearch/cut_ga] ...     ok.
    exercise  104 [    hmmsearch/cut_nc] ...     ok.
    exercise  105 [    hmmsearch/cut_tc] ...     ok.
    exercise  106 [      hmmsearch/domE] ...     ok.
    exercise  107 [      hmmsearch/domT] ...     ok.
    exercise  108 [   hmmsearch/forward] ...     ok.
    exercise  109 [  hmmsearch/informat] ...     ok.
    exercise  110 [     hmmsearch/null2] ...     ok.
    exercise  111 [       hmmsearch/xnu] ...     ok.
    exercise  112 [         align_align] ...     ok.
    exercise  113 [                 evd] ...     ok.
    exercise  114 [               masks] ...     ok.
    exercise  115 [            parsingv] ...     ok.
    exercise  116 [             tophits] ...     ok.
    exercise  117 [               trace] ...     ok.
    exercise  118 [             viterbi] ...     ok.
    exercise  119 [          weeviterbi] ...     ok.
    exercise  120 [    test1/conversion] ...     ok.

All 120 exercises at level <= 2 passed.


System information:
Sun Feb 11 04:10:28 +14 2018
Linux i-capture-the-hostname 4.4.0-57-generic #78-Ubuntu SMP Fri Dec 9 23:48:08 UTC 2016 aarch64 GNU/Linux
make[2]: Leaving directory '/build/hmmer2-2.3.2/2nd/testsuite'
make[1]: Leaving directory '/build/hmmer2-2.3.2/2nd'
 fakeroot debian/rules binary
dh binary --parallel --with autotools-dev
   dh_testroot -O--parallel
   dh_prep -O--parallel
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/hmmer2-2.3.2/2nd'
dh_auto_install -- prefix=/build/hmmer2-2.3.2/2nd/debian/tmp
	make -j8 install DESTDIR=/build/hmmer2-2.3.2/2nd/debian/tmp AM_UPDATE_INFO_DIR=no prefix=/build/hmmer2-2.3.2/2nd/debian/tmp
make[2]: Entering directory '/build/hmmer2-2.3.2/2nd'
mkdir -p /build/hmmer2-2.3.2/2nd/debian/tmp/bin
mkdir -p /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1
for file in hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch hmmcalibrate-pvm hmmpfam-pvm hmmsearch-pvm; do\
   cp src/$file /build/hmmer2-2.3.2/2nd/debian/tmp/bin/;\
done
for file in hmmer hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch; do\
   cp documentation/man/$file.man /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1/$file.1;\
done
make[2]: Leaving directory '/build/hmmer2-2.3.2/2nd'
# lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1:
rename 's/^hmm/hmm2/;' /build/hmmer2-2.3.2/2nd/debian/tmp/bin/*
Deprecated program in use: rename as shipped with the Debian perl package will be removed after the release of stretch. Please install the separate 'rename' package which will provide the same command.
cd /build/hmmer2-2.3.2/2nd/debian/tmp/bin; rename 's/^hmm/hmm2/;' *
Deprecated program in use: rename as shipped with the Debian perl package will be removed after the release of stretch. Please install the separate 'rename' package which will provide the same command.
cd /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' *
Deprecated program in use: rename as shipped with the Debian perl package will be removed after the release of stretch. Please install the separate 'rename' package which will provide the same command.
mv /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1/hmm2er.1 /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1/hmmer2.1
# lkajan: resolve man page hypen issue:
sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' /build/hmmer2-2.3.2/2nd/debian/tmp/share/man/man1/*
make[1]: Leaving directory '/build/hmmer2-2.3.2/2nd'
   dh_install -O--parallel
   dh_installdocs -O--parallel
   debian/rules override_dh_installchangelogs
make[1]: Entering directory '/build/hmmer2-2.3.2/2nd'
dh_installchangelogs -k 00README
make[1]: Leaving directory '/build/hmmer2-2.3.2/2nd'
   debian/rules override_dh_installexamples
make[1]: Entering directory '/build/hmmer2-2.3.2/2nd'
dh_installexamples
mkdir -p /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples;
sed -i "s#hmm#hmm2#g" testsuite/exercises.sqc
rm -f testsuite/*.ssi;
cp -a testsuite/* /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples/;
mkdir /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
cp -a tutorial/* /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples/tutorial;
sed -i "s#../tut#./tut#g" /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples/exercises.sqc
find /build/hmmer2-2.3.2/2nd/debian/hmmer2/usr/share/doc/hmmer2/examples -name 'Makefile' | xargs sed -i "s^/build/hmmer2-2.3.2/2nd^.^g"
make[1]: Leaving directory '/build/hmmer2-2.3.2/2nd'
   dh_installman -O--parallel
   dh_perl -O--parallel
   dh_link -O--parallel
   dh_strip_nondeterminism -O--parallel
   dh_compress -O--parallel
   dh_fixperms -O--parallel
   dh_strip -O--parallel
   dh_makeshlibs -O--parallel
   dh_shlibdeps -O--parallel
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 -O--parallel
   dh_gencontrol -O--parallel
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: 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 hmmer2-doc: unknown substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -O--parallel
   dh_builddeb -O--parallel
dpkg-deb: building package 'hmmer2-pvm-dbgsym' in '../hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb'.
dpkg-deb: building package 'hmmer2-dbgsym' in '../hmmer2-dbgsym_2.3.2-12_arm64.deb'.
dpkg-deb: building package 'hmmer2-doc' in '../hmmer2-doc_2.3.2-12_all.deb'.
dpkg-deb: building package 'hmmer2-pvm' in '../hmmer2-pvm_2.3.2-12_arm64.deb'.
dpkg-deb: building package 'hmmer2' in '../hmmer2_2.3.2-12_arm64.deb'.
 dpkg-genbuildinfo --build=binary
dpkg-genbuildinfo: warning: File::FcntlLock not available; using flock which is not NFS-safe
 dpkg-genchanges --build=binary >../hmmer2_2.3.2-12_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/16942/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/16942/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/16942 and its subdirectories
I: Current time: Sun Feb 11 04:11:05 +14 2018
I: pbuilder-time-stamp: 1518271865
+ PRESULT=0
+ set -e
+ '[' 0 -eq 124 ']'
+ false
+ set +x
Sat Feb 10 14:11:05 UTC 2018  I: Signing ./b2/hmmer2_2.3.2-12_arm64.buildinfo as hmmer2_2.3.2-12_arm64.buildinfo.asc
Sat Feb 10 14:11:05 UTC 2018  I: Signed ./b2/hmmer2_2.3.2-12_arm64.buildinfo as ./b2/hmmer2_2.3.2-12_arm64.buildinfo.asc
Sat Feb 10 14:11:05 UTC 2018 - build #2 for hmmer2/unstable/arm64 on codethink-sled9-arm64 done.
Starting cleanup.
/srv/reproducible-results/rbuild-debian-jQWi6iqM/tmp.VOIB5pulKK:	 56.2% -- replaced with /srv/reproducible-results/rbuild-debian-jQWi6iqM/tmp.VOIB5pulKK.gz
All cleanup done.
Sat Feb 10 14:11:05 UTC 2018 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-Vigr9Yeh, which will now be removed.
/srv/reproducible-results/rbuild-debian-LginDC8w:
total 92
drwxr-xr-x 2 jenkins jenkins  4096 Jan  8 07:45 b1
drwxr-xr-x 2 jenkins jenkins  4096 Jan  8 07:48 b2
-rw-r--r-- 1 jenkins jenkins  2124 Sep  9 20:10 hmmer2_2.3.2-12.dsc
-rw------- 1 jenkins jenkins 77242 Jan  8 07:45 tmp.pWV5woslW5

/srv/reproducible-results/rbuild-debian-LginDC8w/b1:
total 5880
-rw-r--r-- 1 jenkins jenkins   73752 Jan  8 07:45 build.log
-rw-r--r-- 1 jenkins jenkins 2373488 Jan  8 07:45 hmmer2-dbgsym_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins   85856 Jan  8 07:45 hmmer2-doc_2.3.2-12_all.deb
-rw-r--r-- 1 jenkins jenkins  769892 Jan  8 07:45 hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins  120326 Jan  8 07:45 hmmer2-pvm_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins    5539 Jan  8 07:45 hmmer2_2.3.2-12_arm64.buildinfo
-rw-r--r-- 1 jenkins jenkins    6405 Jan  8 07:45 hmmer2_2.3.2-12_arm64.buildinfo.asc
-rw-r--r-- 1 jenkins jenkins    2376 Jan  8 07:45 hmmer2_2.3.2-12_arm64.changes
-rw-r--r-- 1 jenkins jenkins 2539724 Jan  8 07:45 hmmer2_2.3.2-12_arm64.deb

/srv/reproducible-results/rbuild-debian-LginDC8w/b2:
total 6124
-rw-r--r-- 1 jenkins jenkins  326611 Jan  8 07:48 build.log
-rw-r--r-- 1 jenkins jenkins 2373488 Jan  8 07:48 hmmer2-dbgsym_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins   85856 Jan  8 07:48 hmmer2-doc_2.3.2-12_all.deb
-rw-r--r-- 1 jenkins jenkins  769892 Jan  8 07:48 hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins  120326 Jan  8 07:48 hmmer2-pvm_2.3.2-12_arm64.deb
-rw-r--r-- 1 jenkins jenkins    5539 Jan  8 07:48 hmmer2_2.3.2-12_arm64.buildinfo
-rw-r--r-- 1 jenkins jenkins    6405 Jan  8 07:48 hmmer2_2.3.2-12_arm64.buildinfo.asc
-rw-r--r-- 1 jenkins jenkins    2376 Jan  8 07:48 hmmer2_2.3.2-12_arm64.changes
-rw-r--r-- 1 jenkins jenkins 2539724 Jan  8 07:48 hmmer2_2.3.2-12_arm64.deb
Sun Jan  8 07:48:19 UTC 2017  I: hmmer2_2.3.2-12_arm64.changes:
Format: 1.8
Date: Fri, 09 Sep 2016 19:58:20 +0000
Source: hmmer2
Binary: hmmer2 hmmer2-pvm hmmer2-doc
Architecture: arm64 all
Version: 2.3.2-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Changed-By: Sascha Steinbiss <satta at debian.org>
Description:
 hmmer2     - profile hidden Markov models for protein sequence analysis
 hmmer2-doc - profile hidden Markov models for protein sequence analysis (docs)
 hmmer2-pvm - HMMER programs with PVM (Parallel Virtual Machine) support
Changes:
 hmmer2 (2.3.2-12) unstable; urgency=medium
 .
   * Team upload.
   * Make build reproducible.
     - Remove build directory from installed Makefile.
Checksums-Sha1:
 d8a7217ba1d691c44626a71b4ea9b0627293728e 2373488 hmmer2-dbgsym_2.3.2-12_arm64.deb
 968a00208e3d5d020c1f1306b0c9f95ddeb7877b 85856 hmmer2-doc_2.3.2-12_all.deb
 5a13b6fb37b8e9dd8081c907410a1a6a734ebc1f 769892 hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb
 4f4c4a3d667755c64ea8d78f67a04b5d118f55c2 120326 hmmer2-pvm_2.3.2-12_arm64.deb
 7b6c4ec8f29a6a34f979e557b8e207778073d705 5539 hmmer2_2.3.2-12_arm64.buildinfo
 4ec699a6cacf4466386827e9d28092dd377a2125 2539724 hmmer2_2.3.2-12_arm64.deb
Checksums-Sha256:
 f9bdf7caadcba2444aa77609846839a31631303ca334cf4193bd3bc2d58d7231 2373488 hmmer2-dbgsym_2.3.2-12_arm64.deb
 cbfb9b670043f68ffd72c9933c989aa3db32cf4e57a0bbfe9bf5cf7800f72f95 85856 hmmer2-doc_2.3.2-12_all.deb
 c83355b3db70c872b3dd46ae190bf3faf3fc7a5160f5ea4e55b59fba13ee6faf 769892 hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb
 1461f3b6f55462727bfefff8d607b313b47f01bb0aad1d916c87744988bad9a6 120326 hmmer2-pvm_2.3.2-12_arm64.deb
 0732d4653bf771babc72106bd738e34a9f4a9a0528a7ae6ba3712cc57047b070 5539 hmmer2_2.3.2-12_arm64.buildinfo
 2683ad372cb414dd6ea8f5f905b50b788077a399b33576c0d2e702eb3bc4bbce 2539724 hmmer2_2.3.2-12_arm64.deb
Files:
 367a932574bb7b7d8b242c361397ced2 2373488 debug extra hmmer2-dbgsym_2.3.2-12_arm64.deb
 bdd9566739c0d5c28fcf5e5b13f696a3 85856 doc optional hmmer2-doc_2.3.2-12_all.deb
 c3eeb03743893eb61e7ecbb73ce981fc 769892 debug extra hmmer2-pvm-dbgsym_2.3.2-12_arm64.deb
 9deafee9386301e45c0d1271f0899f88 120326 science optional hmmer2-pvm_2.3.2-12_arm64.deb
 2ba7332d957a8494d1e729dc9b34f99a 5539 science optional hmmer2_2.3.2-12_arm64.buildinfo
 3fe75a71b1f4dee21b4d188ae1482fcd 2539724 science optional hmmer2_2.3.2-12_arm64.deb
removed ‘/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hmmer2_2.3.2-12.diff’
Diff of the two buildlogs:

--
tee: /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/hmmer2_2.3.2-12.diff: No space left on device
Starting cleanup.
/srv/reproducible-results/rbuild-debian-LginDC8w/tmp.pWV5woslW5:	 84.1% -- replaced with /srv/reproducible-results/rbuild-debian-LginDC8w/tmp.pWV5woslW5.gz
INFO: Starting at 2017-01-08 07:48:19.899343
INFO: Finished at 2017-01-08 07:48:20.175666, took: 0:00:00.276338
All cleanup done.
Sun  8 Jan 07:48:20 UTC 2017 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-0J2Yge5F, which will now be removed.
Build step 'Execute shell' marked build as failure

More information about the Qa-jenkins-scm mailing list