0s autopkgtest [09:48:57]: starting date: 2024-01-09
  0s autopkgtest [09:48:57]: git checkout: f7cd36b ssh-setup/nova: fix ARCH having two lines of data
  0s autopkgtest [09:48:57]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ofleep98/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:bamtools --apt-upgrade bamtools --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=bamtools/2.5.2+dfsg-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-s390x-2.secgroup --name adt-noble-s390x-bamtools-20240109-093249-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/
 74s autopkgtest [09:50:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup
 75s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [118 kB]
 75s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [7916 B]
 75s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [41.3 kB]
 75s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [334 kB]
 75s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [51.9 kB]
 75s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B]
 75s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B]
 75s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [215 kB]
 75s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B]
 75s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [1716 B]
 75s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B]
 76s Fetched 780 kB in 1s (1044 kB/s)
 76s Reading package lists...
 79s Reading package lists...
 79s Building dependency tree...
 79s Reading state information...
 79s Calculating upgrade...
 79s The following packages will be upgraded:
 79s   irqbalance logrotate
 79s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 79s Need to get 112 kB of archives.
 79s After this operation, 5120 B disk space will be freed.
 79s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x irqbalance s390x 1.9.3-2ubuntu1 [50.9 kB]
 80s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x logrotate s390x 3.21.0-2 [60.6 kB]
 80s Fetched 112 kB in 0s (312 kB/s)
 80s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 45%
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(Reading database ... 55%
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(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75573 files and directories currently installed.)
 80s Preparing to unpack .../irqbalance_1.9.3-2ubuntu1_s390x.deb ...
 80s Unpacking irqbalance (1.9.3-2ubuntu1) over (1.9.3-1) ...
 80s Preparing to unpack .../logrotate_3.21.0-2_s390x.deb ...
 80s Unpacking logrotate (3.21.0-2) over (3.21.0-1) ...
 80s Setting up logrotate (3.21.0-2) ...
 81s logrotate.service is a disabled or a static unit not running, not starting it.
 81s Setting up irqbalance (1.9.3-2ubuntu1) ...
 82s Processing triggers for man-db (2.12.0-1) ...
 83s Reading package lists...
 83s Building dependency tree...
 83s Reading state information...
 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 84s sh: Attempting to set up Debian/Ubuntu apt sources automatically
 84s sh: Distribution appears to be Ubuntu
 85s Reading package lists...
 85s Building dependency tree...
 85s Reading state information...
 86s eatmydata is already the newest version (131-1).
 86s dbus is already the newest version (1.14.10-1ubuntu1).
 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 86s Reading package lists...
 86s Building dependency tree...
 86s Reading state information...
 87s rng-tools-debian is already the newest version (2.4).
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 87s Reading package lists...
 87s Building dependency tree...
 87s Reading state information...
 87s haveged is already the newest version (1.9.14-1ubuntu1).
 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 88s Reading package lists...
 88s Building dependency tree...
 88s Reading state information...
 88s The following packages will be REMOVED:
 88s   cloud-init* isc-dhcp-client* isc-dhcp-common* python3-configobj*
 88s   python3-debconf*
 88s 0 upgraded, 0 newly installed, 5 to remove and 0 not upgraded.
 88s After this operation, 4204 kB disk space will be freed.
 88s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75572 files and directories currently installed.)
 88s Removing cloud-init (24.1~2gb6a1c635-0ubuntu1) ...
 89s Removing isc-dhcp-client (4.4.3-P1-4ubuntu1) ...
 89s Removing isc-dhcp-common (4.4.3-P1-4ubuntu1) ...
 89s Removing python3-configobj (5.0.8-2) ...
 89s Removing python3-debconf (1.5.82) ...
 89s Processing triggers for man-db (2.12.0-1) ...
 90s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 20%
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(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75158 files and directories currently installed.)
 90s Purging configuration files for cloud-init (24.1~2gb6a1c635-0ubuntu1) ...
 90s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed
 90s Purging configuration files for isc-dhcp-client (4.4.3-P1-4ubuntu1) ...
 90s Processing triggers for rsyslog (8.2306.0-2ubuntu2) ...
 91s Reading package lists...
 91s Building dependency tree...
 91s Reading state information...
 91s linux-generic is already the newest version (6.6.0-14.14).
 91s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 92s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease
 92s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease
 92s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease
 92s Hit:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease
 93s Reading package lists...
 93s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 94s Calculating upgrade...
 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 94s Reading package lists...
 94s Building dependency tree...
 94s Reading state information...
 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 95s autopkgtest [09:50:32]: rebooting testbed after setup commands that affected boot
109s autopkgtest [09:50:46]: testbed running kernel: Linux 6.6.0-14-generic #14-Ubuntu SMP Thu Nov 30 09:46:34 UTC 2023
110s autopkgtest [09:50:47]: testbed dpkg architecture: s390x
111s autopkgtest [09:50:48]: @@@@@@@@@@@@@@@@@@@@ apt-source bamtools
114s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe bamtools 2.5.2+dfsg-5 (dsc) [2513 B]
114s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe bamtools 2.5.2+dfsg-5 (tar) [156 kB]
114s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe bamtools 2.5.2+dfsg-5 (diff) [10.4 kB]
114s gpgv: Signature made Fri Dec 15 18:13:56 2023 UTC
114s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
114s gpgv:                issuer "emollier@debian.org"
114s gpgv: Can't check signature: No public key
114s dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-5.dsc: no acceptable signature found
114s autopkgtest [09:50:51]: testing package bamtools version 2.5.2+dfsg-5
114s autopkgtest [09:50:51]: build not needed
118s autopkgtest [09:50:55]: test run-unit-test: preparing testbed
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
120s Correcting dependencies...Starting pkgProblemResolver with broken count: 0
121s Starting 2 pkgProblemResolver with broken count: 0
121s Done
121s  Done
121s Starting pkgProblemResolver with broken count: 0
121s Starting 2 pkgProblemResolver with broken count: 0
121s Done
122s The following additional packages will be installed:
122s   bamtools libbamtools-dev libbamtools-doc libbamtools2.5.2 libc-dev-bin
122s   libc6-dev libcrypt-dev libjs-jquery libjsoncpp25 libnsl-dev libtirpc-dev
122s   linux-libc-dev rpcsvc-proto zlib1g-dev
122s Suggested packages:
122s   glibc-doc manpages-dev
122s Recommended packages:
122s   manpages manpages-dev libc-devtools javascript-common
122s The following NEW packages will be installed:
122s   bamtools libbamtools-dev libbamtools-doc libbamtools2.5.2 libc-dev-bin
122s   libc6-dev libcrypt-dev libjs-jquery libjsoncpp25 libnsl-dev libtirpc-dev
122s   linux-libc-dev rpcsvc-proto zlib1g-dev
122s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded.
122s 1 not fully installed or removed.
122s Need to get 5697 kB of archives.
122s After this operation, 25.7 MB of additional disk space will be used.
122s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbamtools2.5.2 s390x 2.5.2+dfsg-5 [142 kB]
122s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libjsoncpp25 s390x 1.9.5-6 [75.5 kB]
122s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x bamtools s390x 2.5.2+dfsg-5 [173 kB]
122s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libc-dev-bin s390x 2.38-3ubuntu1 [20.0 kB]
122s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x linux-libc-dev s390x 6.6.0-14.14 [1576 kB]
123s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x libcrypt-dev s390x 1:4.4.36-2 [117 kB]
123s Get:7 http://ftpmaster.internal/ubuntu noble/main s390x libtirpc-dev s390x 1.3.4+ds-1 [196 kB]
123s Get:8 http://ftpmaster.internal/ubuntu noble/main s390x libnsl-dev s390x 1.3.0-3 [73.5 kB]
123s Get:9 http://ftpmaster.internal/ubuntu noble/main s390x rpcsvc-proto s390x 1.4.2-0ubuntu6 [64.7 kB]
123s Get:10 http://ftpmaster.internal/ubuntu noble/main s390x libc6-dev s390x 2.38-3ubuntu1 [1626 kB]
123s Get:11 http://ftpmaster.internal/ubuntu noble/main s390x zlib1g-dev s390x 1:1.3.dfsg-3ubuntu1 [905 kB]
123s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbamtools-dev s390x 2.5.2+dfsg-5 [242 kB]
123s Get:13 http://ftpmaster.internal/ubuntu noble/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
123s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x libbamtools-doc all 2.5.2+dfsg-5 [159 kB]
123s Fetched 5697 kB in 1s (6677 kB/s)
123s Selecting previously unselected package libbamtools2.5.2:s390x.
123s (Reading database ... 
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(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 75093 files and directories currently installed.)
123s Preparing to unpack .../00-libbamtools2.5.2_2.5.2+dfsg-5_s390x.deb ...
123s Unpacking libbamtools2.5.2:s390x (2.5.2+dfsg-5) ...
123s Selecting previously unselected package libjsoncpp25:s390x.
123s Preparing to unpack .../01-libjsoncpp25_1.9.5-6_s390x.deb ...
123s Unpacking libjsoncpp25:s390x (1.9.5-6) ...
123s Selecting previously unselected package bamtools.
123s Preparing to unpack .../02-bamtools_2.5.2+dfsg-5_s390x.deb ...
123s Unpacking bamtools (2.5.2+dfsg-5) ...
123s Selecting previously unselected package libc-dev-bin.
123s Preparing to unpack .../03-libc-dev-bin_2.38-3ubuntu1_s390x.deb ...
123s Unpacking libc-dev-bin (2.38-3ubuntu1) ...
123s Selecting previously unselected package linux-libc-dev:s390x.
123s Preparing to unpack .../04-linux-libc-dev_6.6.0-14.14_s390x.deb ...
123s Unpacking linux-libc-dev:s390x (6.6.0-14.14) ...
123s Selecting previously unselected package libcrypt-dev:s390x.
123s Preparing to unpack .../05-libcrypt-dev_1%3a4.4.36-2_s390x.deb ...
123s Unpacking libcrypt-dev:s390x (1:4.4.36-2) ...
123s Selecting previously unselected package libtirpc-dev:s390x.
123s Preparing to unpack .../06-libtirpc-dev_1.3.4+ds-1_s390x.deb ...
123s Unpacking libtirpc-dev:s390x (1.3.4+ds-1) ...
124s Selecting previously unselected package libnsl-dev:s390x.
124s Preparing to unpack .../07-libnsl-dev_1.3.0-3_s390x.deb ...
124s Unpacking libnsl-dev:s390x (1.3.0-3) ...
124s Selecting previously unselected package rpcsvc-proto.
124s Preparing to unpack .../08-rpcsvc-proto_1.4.2-0ubuntu6_s390x.deb ...
124s Unpacking rpcsvc-proto (1.4.2-0ubuntu6) ...
124s Selecting previously unselected package libc6-dev:s390x.
124s Preparing to unpack .../09-libc6-dev_2.38-3ubuntu1_s390x.deb ...
124s Unpacking libc6-dev:s390x (2.38-3ubuntu1) ...
124s Selecting previously unselected package zlib1g-dev:s390x.
124s Preparing to unpack .../10-zlib1g-dev_1%3a1.3.dfsg-3ubuntu1_s390x.deb ...
124s Unpacking zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ...
124s Selecting previously unselected package libbamtools-dev:s390x.
124s Preparing to unpack .../11-libbamtools-dev_2.5.2+dfsg-5_s390x.deb ...
124s Unpacking libbamtools-dev:s390x (2.5.2+dfsg-5) ...
124s Selecting previously unselected package libjs-jquery.
124s Preparing to unpack .../12-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
124s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
124s Selecting previously unselected package libbamtools-doc.
124s Preparing to unpack .../13-libbamtools-doc_2.5.2+dfsg-5_all.deb ...
124s Unpacking libbamtools-doc (2.5.2+dfsg-5) ...
124s Setting up linux-libc-dev:s390x (6.6.0-14.14) ...
124s Setting up libtirpc-dev:s390x (1.3.4+ds-1) ...
124s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ...
124s Setting up libjsoncpp25:s390x (1.9.5-6) ...
124s Setting up libbamtools2.5.2:s390x (2.5.2+dfsg-5) ...
124s Setting up libnsl-dev:s390x (1.3.0-3) ...
124s Setting up libcrypt-dev:s390x (1:4.4.36-2) ...
124s Setting up bamtools (2.5.2+dfsg-5) ...
124s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
124s Setting up libc-dev-bin (2.38-3ubuntu1) ...
124s Setting up libbamtools-doc (2.5.2+dfsg-5) ...
124s Setting up libc6-dev:s390x (2.38-3ubuntu1) ...
124s Setting up zlib1g-dev:s390x (1:1.3.dfsg-3ubuntu1) ...
124s Setting up libbamtools-dev:s390x (2.5.2+dfsg-5) ...
124s Setting up autopkgtest-satdep (0) ...
124s Processing triggers for man-db (2.12.0-1) ...
125s Processing triggers for libc-bin (2.38-3ubuntu1) ...
128s (Reading database ... 77202 files and directories currently installed.)
128s Removing autopkgtest-satdep (0) ...
129s autopkgtest [09:51:06]: test run-unit-test: [-----------------------
130s 6
130s The following test is known to time out on s390x architecture (see bug #953939)
130s bamtools filter -script filter_script -in sam_spec_example.bam -out out.bam
130s /tmp/autopkgtest.lfdPaP/build.FDz/src/debian/tests/run-unit-test: 27: [: armel-a: unexpected operator
130s @HD	VN:1.5	SO:coordinate
130s @SQ	SN:ref	LN:45
130s 
130s *** buffer overflow detected ***: terminated
130s Aborted (core dumped)
130s autopkgtest [09:51:07]: test run-unit-test: -----------------------]
131s run-unit-test        FAIL non-zero exit status 134
131s autopkgtest [09:51:08]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
131s autopkgtest [09:51:08]: @@@@@@@@@@@@@@@@@@@@ summary
131s run-unit-test        FAIL non-zero exit status 134
143s Creating nova instance adt-noble-s390x-bamtools-20240109-093249-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-s390x-server-20240109.img (UUID ab0d9ea4-bb9c-4c88-9d54-a47227217f73)...