Build failed in Jenkins: raring-adt-bowtie2-armhf » armhf,adt&&arm #2

Jenkins Notification devnull at canonical.com
Fri Apr 5 14:21:53 UTC 2013 

See <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/2/>

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[...truncated 441 lines...]
adt-run: trace1: $     rm -rf -- "$TMPDIR"
adt-run: trace1: $     export TMPDIR
adt-run: trace1: $     su ubuntu -c 'mkdir -- "$TMPDIR"'
adt-run: trace1: $     spec="$spec" origpwd="$origpwd" su ubuntu -c '
adt-run: trace1: $     			dpkg-source -x $spec
adt-run: trace1: $     			'
adt-run: trace1: $     cd [a-z0-9]*-*/.
adt-run: trace1: $     pwd >&3
adt-run: trace1: $     set +e; test -f debian/tests/control; echo $? >&3
+ spec=/tmp/tmp.s5x6gmuocj/dsc0/bowtie2_2.0.5-1.dsc
+ pwd
+ origpwd=/tmp/tmp.s5x6gmuocj/dsc0-build
+ cd /tmp/tmp.s5x6gmuocj/dsc0-build
+ chown ubuntu . ..
+ TMPDIR=/tmp/tmp.s5x6gmuocj/dsc0-build/tmpdir
+ rm -rf -- /tmp/tmp.s5x6gmuocj/dsc0-build/tmpdir
+ export TMPDIR
+ su ubuntu -c mkdir -- "$TMPDIR"
+ spec=/tmp/tmp.s5x6gmuocj/dsc0/bowtie2_2.0.5-1.dsc origpwd=/tmp/tmp.s5x6gmuocj/dsc0-build su ubuntu -c 
			dpkg-source -x $spec
			
gpgv: Signature made Fri 11 Jan 2013 10:52:29 AM UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on /tmp/tmp.s5x6gmuocj/dsc0/bowtie2_2.0.5-1.dsc
dpkg-source: info: extracting bowtie2 in bowtie2-2.0.5
dpkg-source: info: unpacking bowtie2_2.0.5.orig.tar.gz
dpkg-source: info: unpacking bowtie2_2.0.5-1.debian.tar.gz
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying fix_makefile_machine_detection.patch
+ cd bowtie2-2.0.5/.
+ pwd
+ set +e
+ test -f debian/tests/control
+ echo 0
adt-run: trace: & dsc0t-indexing_ref_genome: constructed; path=debian/tests/indexing_ref_genome
adt-run: trace: & dsc0t-indexing_ref_genome:  .depends=@
adt-run: trace: * <dsc:dsc0> build not needed
adt-run: trace: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ builds done.
adt-run: trace: * reset
adt-run: trace: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests ...
adt-run: trace: @@@@@@@@@@@@@@@@@@@@ test dsc dsc0
adt-run: trace1: ** needs_reset, previously=True
adt-run: trace: @@@@@@@@@@ read control ...
adt-run: trace: & dsc0t-indexing_ref_genome: constructed; path=debian/tests/indexing_ref_genome
adt-run: trace: & dsc0t-indexing_ref_genome:  .depends=@
adt-run: trace: @@@@@@@@@@ run_tests ...
adt-run: trace: & dsc0t-indexing_ref_genome: preparing
adt-run: trace: & dsc0t-indexing_ref_genome:  processing dependency @
adt-run: trace: & dsc0t-indexing_ref_genome:   synthesised dependency bowtie2-examples
adt-run: trace1: ** prepare1, modified=True, deps_processed=[], deps_new=['bowtie2-examples']
adt-run: trace1: ** prepare2, deps_new=['bowtie2-examples']
adt-run: trace: * publish
adt-run: trace: $ ftparchive: sh -ec <SCRIPT> x /home/ubuntu/adt-log//binaries /home/ubuntu/.autopkgtest/gpg
adt-run: trace1: $     
adt-run: trace1: $       exec >&2
adt-run: trace1: $       cd "$1"
adt-run: trace1: $       apt-ftparchive packages . >Packages
adt-run: trace1: $       gzip <Packages >Packages.gz
adt-run: trace1: $       apt-ftparchive release . >Release
adt-run: trace1: $       rm -f Release.gpg
adt-run: trace1: $       gpg --homedir="$2" --batch --detach-sign --armour -o Release.gpg Release
adt-run: trace1: $       gpg --homedir="$2" --batch --export >archive-key.pgp
adt-run: trace1: $     		
adt-run: trace: $ apt-key: sh -ec <SCRIPT>
adt-run: trace1: $     
adt-run: trace1: $       exec 3>&1 >&2
adt-run: trace1: $       apt-key add archive-key.pgp
adt-run: trace1: $       echo "deb file:///tmp/tmp.s5x6gmuocj/binaries/ /" >/etc/apt/sources.list.d/autopkgtest.list
adt-run: trace1: $       if [ "x`ls /var/lib/dpkg/updates`" != x ]; then
adt-run: trace1: $         echo >&2 "/var/lib/dpkg/updates contains some files, aargh"; exit 1
adt-run: trace1: $       fi
adt-run: trace1: $       apt-get -q -o quiet=true -o APT::Get::Assume-Yes=true -o Debug::pkgProblemResolver=true -o APT::Get::force-yes=true update >&2
adt-run: trace1: $       cat /var/lib/dpkg/status >&3
adt-run: trace1: $     		
OK
Get:1 file:  Release.gpg [198 B]
Get:2 file:  Release [1,202 B]
Ign file:  Translation-en_US
Ign file:  Translation-en
Hit http://archive.ubuntu.com raring Release.gpg
Hit http://ports.ubuntu.com raring Release.gpg
Hit http://archive.ubuntu.com raring-proposed Release.gpg
Hit http://ports.ubuntu.com raring-updates Release.gpg
Hit http://archive.ubuntu.com raring Release
Hit http://ports.ubuntu.com raring-security Release.gpg
Hit http://ports.ubuntu.com raring-proposed Release.gpg
Hit http://archive.ubuntu.com raring-proposed Release
Hit http://ports.ubuntu.com raring Release
Hit http://archive.ubuntu.com raring/restricted Sources
Hit http://ports.ubuntu.com raring-updates Release
Hit http://archive.ubuntu.com raring/multiverse Sources
Hit http://ports.ubuntu.com raring-security Release
Hit http://archive.ubuntu.com raring-proposed/main Sources
Hit http://ports.ubuntu.com raring-proposed Release
Hit http://archive.ubuntu.com raring-proposed/restricted Sources
Hit http://ports.ubuntu.com raring/main Sources
Hit http://archive.ubuntu.com raring-proposed/universe Sources
Hit http://ports.ubuntu.com raring/universe Sources
Hit http://archive.ubuntu.com raring-proposed/multiverse Sources
Hit http://ports.ubuntu.com raring/main armhf Packages
Hit http://ports.ubuntu.com raring/universe armhf Packages
Hit http://ports.ubuntu.com raring/restricted armhf Packages
Hit http://ports.ubuntu.com raring/multiverse armhf Packages
Hit http://ports.ubuntu.com raring/main Translation-en
Hit http://ports.ubuntu.com raring/multiverse Translation-en
Hit http://ports.ubuntu.com raring/restricted Translation-en
Hit http://ports.ubuntu.com raring/universe Translation-en
Hit http://ports.ubuntu.com raring-updates/main Sources
Hit http://ports.ubuntu.com raring-updates/universe Sources
Hit http://ports.ubuntu.com raring-updates/main armhf Packages
Hit http://ports.ubuntu.com raring-updates/universe armhf Packages
Hit http://ports.ubuntu.com raring-updates/main Translation-en
Hit http://ports.ubuntu.com raring-updates/universe Translation-en
Hit http://ports.ubuntu.com raring-security/main Sources
Hit http://ports.ubuntu.com raring-security/universe Sources
Hit http://ports.ubuntu.com raring-security/main armhf Packages
Hit http://ports.ubuntu.com raring-security/universe armhf Packages
Hit http://ports.ubuntu.com raring-security/main Translation-en
Hit http://ports.ubuntu.com raring-security/universe Translation-en
Hit http://ports.ubuntu.com raring-proposed/restricted armhf Packages
Hit http://ports.ubuntu.com raring-proposed/main armhf Packages
Hit http://ports.ubuntu.com raring-proposed/multiverse armhf Packages
Hit http://ports.ubuntu.com raring-proposed/universe armhf Packages
Hit http://ports.ubuntu.com raring-proposed/main Translation-en
Hit http://ports.ubuntu.com raring-proposed/multiverse Translation-en
Hit http://ports.ubuntu.com raring-proposed/restricted Translation-en
Hit http://ports.ubuntu.com raring-proposed/universe Translation-en
Ign http://ports.ubuntu.com raring/main Translation-en_US
Ign http://ports.ubuntu.com raring/multiverse Translation-en_US
Ign http://ports.ubuntu.com raring/restricted Translation-en_US
Ign http://ports.ubuntu.com raring/universe Translation-en_US
Ign http://ports.ubuntu.com raring-updates/main Translation-en_US
Ign http://ports.ubuntu.com raring-updates/universe Translation-en_US
Ign http://ports.ubuntu.com raring-security/main Translation-en_US
Ign http://ports.ubuntu.com raring-security/universe Translation-en_US
Ign http://ports.ubuntu.com raring-proposed/main Translation-en_US
Ign http://ports.ubuntu.com raring-proposed/multiverse Translation-en_US
Ign http://ports.ubuntu.com raring-proposed/restricted Translation-en_US
Ign http://ports.ubuntu.com raring-proposed/universe Translation-en_US
Reading package lists...adt-run: trace: * publish reinstall checking...

adt-run: trace: * publish install...
adt-run: trace: * publish done
adt-run: trace1: **  installing dependencies ['bowtie2-examples']
adt-run: trace: dependencies: install-deps: satisfying bowtie2-examples
adt-run: trace: dependencies: install-deps: running ['/usr/lib/pbuilder/pbuilder-satisfydepends-classic', '--binary-all', '--internal-chrootexec', '/home/ubuntu/adt-log//satdep-auxverb', '-c', '/home/ubuntu/adt-log//deps.dsc']
 -> Attempting to parse the build-deps 
 -> Considering build-dep bowtie2-examples
   -> Trying bowtie2-examples
 -> Installing  bowtie2-examples
Reading package lists...
Building dependency tree...
Reading state information...
Recommended packages:
  bowtie2
The following NEW packages will be installed:
  bowtie2-examples
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 4,877 kB of archives.
After this operation, 4,962 kB of additional disk space will be used.
Get:1 http://ports.ubuntu.com/ubuntu-ports/ raring/universe bowtie2-examples all 2.0.5-1 [4,877 kB]
Fetched 4,877 kB in 3s (1,360 kB/s)
Selecting previously unselected package bowtie2-examples.
(Reading database ... 61639 files and directories currently installed.)
Unpacking bowtie2-examples (from .../bowtie2-examples_2.0.5-1_all.deb) ...
Setting up bowtie2-examples (2.0.5-1) ...
 -> Finished parsing the build-deps
adt-run: trace: & dsc0t-indexing_ref_genome: [----------------------------------------
+ buildtree=/tmp/tmp.s5x6gmuocj/dsc0-build/bowtie2-2.0.5/
+ shift
+ rm -rf -- /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/tmpdir /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/adttmp
+ mkdir -- /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/tmpdir /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/adttmp
+ chown ubuntu /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/tmpdir /tmp/tmp.s5x6gmuocj/dsc0t-indexing_ref_genome-testtmp/adttmp
adt-run: trace: & dsc0t-indexing_ref_genome:  - - - - - - - - - - results - - - - - - - - - -
dsc0t-indexing_ref_genome FAIL non-zero exit status 127
adt-run: trace: & dsc0t-indexing_ref_genome: ----------------------------------------]
adt-run: trace1: ** needs_reset, previously=False
adt-run: trace: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ tests done.
adt-run: trace: ** stop
adt-run: trace: ** close, scratch=tb-scratch~/tmp/tmp.s5x6gmuocj:-/|/tmp/tmp.s5x6gmuocj/!
+ RC=4
+ [ 4 -eq 20 ]
+ [ 0 -eq 1 ]
+ [ -x /home/ubuntu/adt-export-result ]
+ RES=PASS
+ [ 4 -gt 0 ]
+ RES=FAIL
+ /home/ubuntu/adt-export-result -D /home/ubuntu/adt-log bowtie2 FAIL
+ chown -R ubuntu /home/ubuntu/adt-log /var/tmp/testresults
+ chmod og+r /var/log/syslog
+ chmod og+r /var/crash/*
+ true
+ exit 4
+ RET=4
+ [ 0 -eq 1 ]
+ [ 4 -gt 0 ]
+ log_failure_msg adt-run exited with status 4.
+ log_msg Failure: adt-run exited with status 4.\n
+ date +%F %X
+ printf 2013-04-05 10:21:39: Failure: adt-run exited with status 4.\n
2013-04-05 10:21:39: Failure: adt-run exited with status 4.
+ [ 0 -eq 0 ]
+ mkdir -p <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results>
+ ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o CheckHostIP=no -i /home/auto-package-testing/adt/disks/adtkey -p 22 -t -o BatchMode=yes -l ubuntu pristine-adt-raring-armhf-2ahraf.lxc sudo chown -R ubuntu /home/ubuntu/adt-log; find /home/ubuntu/adt-log -type f -empty | xargs rm
Pseudo-terminal will not be allocated because stdin is not a terminal.
Warning: Permanently added 'pristine-adt-raring-armhf-2ahraf.lxc' (ECDSA) to the list of known hosts.
+ scp -r -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o CheckHostIP=no -i /home/auto-package-testing/adt/disks/adtkey -P 22 ubuntu at pristine-adt-raring-armhf-2ahraf.lxc:/home/ubuntu/adt-log/* /var/crash/*crash /var/log/syslog /var/tmp/testresults <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results>
+ true
+ log_info_msg Test artifacts copied to <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results>
+ log_msg Info: Test artifacts copied to <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results\n>
+ date +%F %X
+ printf 2013-04-05 10:21:49: Info: Test artifacts copied to <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results\n>
2013-04-05 10:21:49: Info: Test artifacts copied to <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results>
+ [ -n 2013-04-05_14-12-59 ]
+ log_info_msg Updating Jenkins results
+ log_msg Info: Updating Jenkins results\n
+ date +%F %X
+ printf 2013-04-05 10:21:49: Info: Updating Jenkins results\n
2013-04-05 10:21:49: Info: Updating Jenkins results
+ rsync -a <http://10.189.74.2:8080/job/raring-adt-bowtie2-armhf/./ARCH=armhf,label=adt&&arm/ws/results/raring_armv7l_bowtie2_20130405-142138.result> /raring/out/
rsync: mkdir "/raring/out" failed: No such file or directory (2)
rsync error: error in file IO (code 11) at main.c(605) [Receiver=3.0.9]
rsync: connection unexpectedly closed (9 bytes received so far) [sender]
rsync error: error in rsync protocol data stream (code 12) at io.c(605) [sender=3.0.9]
+ true
+ [ 0 -eq 0 ]
+ ssh -o UserKnownHostsFile=/dev/null -o StrictHostKeyChecking=no -o CheckHostIP=no -i /home/auto-package-testing/adt/disks/adtkey -p 22 -t -o BatchMode=yes -l ubuntu pristine-adt-raring-armhf-2ahraf.lxc sudo poweroff
Pseudo-terminal will not be allocated because stdin is not a terminal.
Warning: Permanently added 'pristine-adt-raring-armhf-2ahraf.lxc' (ECDSA) to the list of known hosts.
+ exit 4
+ on_exit
+ log_info_msg Cleaning up
+ log_msg Info: Cleaning up\n
+ date +%F %X
+ printf 2013-04-05 10:21:51: Info: Cleaning up\n
2013-04-05 10:21:51: Info: Cleaning up
+ [ -d /tmp/adt-armhf.ltBBBh ]
+ rm -Rf /tmp/adt-armhf.ltBBBh
+ sudo lxc-stop -n pristine-adt-raring-armhf-2ahraf
+ LOOP=0
+ :
+ LOOP=10
+ [ 10 -gt 120 ]
+ sudo lxc-info -n pristine-adt-raring-armhf-2ahraf -t STOPPED
+ break
+ sudo lxc-destroy -n pristine-adt-raring-armhf-2ahraf
+ exit 4
Build step 'Execute shell' marked build as failure
Archiving artifacts

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