0s autopkgtest [19:36:46]: starting date and time: 2025-03-15 19:36:46+0000
  0s autopkgtest [19:36:46]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production'
  0s autopkgtest [19:36:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.mj972eza/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-28.secgroup --name adt-plucky-s390x-uncalled-20250315-193645-juju-7f2275-prod-proposed-migration-environment-2-499559dd-364e-48fd-8334-fb8196b0e427 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
103s autopkgtest [19:38:29]: testbed dpkg architecture: s390x
103s autopkgtest [19:38:29]: testbed apt version: 2.9.33
104s autopkgtest [19:38:30]: @@@@@@@@@@@@@@@@@@@@ test bed setup
104s autopkgtest [19:38:30]: testbed release detected to be: None
105s autopkgtest [19:38:31]: updating testbed package index (apt update)
105s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB]
105s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
105s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [369 kB]
106s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.5 kB]
106s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [45.1 kB]
106s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [77.3 kB]
106s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B]
106s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B]
106s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [314 kB]
106s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.3 kB]
106s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3532 B]
106s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B]
106s Fetched 965 kB in 1s (1040 kB/s)
106s Reading package lists...
107s Reading package lists...
107s Building dependency tree...
107s Reading state information...
107s Calculating upgrade...
107s Calculating upgrade...
108s The following packages were automatically installed and are no longer required:
108s   libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64
108s   linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic
108s   linux-modules-6.11.0-8-generic linux-tools-6.11.0-8
108s   linux-tools-6.11.0-8-generic
108s Use 'sudo apt autoremove' to remove them.
108s The following packages will be upgraded:
108s   pinentry-curses python3-jinja2 strace
108s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
108s Need to get 652 kB of archives.
108s After this operation, 27.6 kB of additional disk space will be used.
108s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB]
108s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB]
108s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB]
109s Fetched 652 kB in 1s (858 kB/s)
109s (Reading database ... 
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(Reading database ... 81428 files and directories currently installed.)
109s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ...
109s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ...
109s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ...
109s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ...
109s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ...
109s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ...
109s Setting up pinentry-curses (1.3.1-2ubuntu3) ...
109s Setting up python3-jinja2 (3.1.5-2ubuntu1) ...
109s Setting up strace (6.13+ds-1ubuntu1) ...
109s Processing triggers for man-db (2.13.0-1) ...
109s Reading package lists...
110s Building dependency tree...
110s Reading state information...
110s Solving dependencies...
110s The following packages will be REMOVED:
110s   libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64*
110s   linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic*
110s   linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8*
110s   linux-tools-6.11.0-8-generic*
110s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded.
110s After this operation, 167 MB disk space will be freed.
110s (Reading database ... 
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(Reading database ... 81428 files and directories currently installed.)
110s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ...
110s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ...
110s Removing libpython3.12t64:s390x (3.12.9-1) ...
110s Removing libpython3.12-stdlib:s390x (3.12.9-1) ...
110s Removing libnsl2:s390x (1.3.0-3build3) ...
110s Removing libpython3.12-minimal:s390x (3.12.9-1) ...
110s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ...
110s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ...
111s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
111s Processing triggers for libc-bin (2.41-1ubuntu1) ...
111s (Reading database ... 
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(Reading database ... 56328 files and directories currently installed.)
111s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ...
111s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ...
111s autopkgtest [19:38:37]: upgrading testbed (apt dist-upgrade and autopurge)
111s Reading package lists...
112s Building dependency tree...
112s Reading state information...
112s Calculating upgrade...Starting pkgProblemResolver with broken count: 0
112s Starting 2 pkgProblemResolver with broken count: 0
112s Done
112s Entering ResolveByKeep
112s 
112s Calculating upgrade...
112s The following packages will be upgraded:
112s   libc-bin libc-dev-bin libc6 libc6-dev locales
112s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
112s Need to get 9512 kB of archives.
112s After this operation, 8192 B of additional disk space will be used.
112s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB]
113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB]
113s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB]
113s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB]
113s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB]
114s Preconfiguring packages ...
114s Fetched 9512 kB in 2s (5436 kB/s)
114s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
114s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ...
114s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
114s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ...
114s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
114s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ...
114s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
114s Setting up libc6:s390x (2.41-1ubuntu2) ...
115s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 56326 files and directories currently installed.)
115s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ...
115s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
115s Setting up libc-bin (2.41-1ubuntu2) ...
115s (Reading database ... 
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 56326 files and directories currently installed.)
115s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ...
115s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ...
115s Setting up locales (2.41-1ubuntu2) ...
115s Generating locales (this might take a while)...
116s   en_US.UTF-8... done
116s Generation complete.
116s Setting up libc-dev-bin (2.41-1ubuntu2) ...
116s Setting up libc6-dev:s390x (2.41-1ubuntu2) ...
116s Processing triggers for man-db (2.13.0-1) ...
117s Processing triggers for systemd (257.3-1ubuntu3) ...
117s Reading package lists...
118s Building dependency tree...
118s Reading state information...
118s Starting pkgProblemResolver with broken count: 0
118s Starting 2 pkgProblemResolver with broken count: 0
118s Done
118s Solving dependencies...
118s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
118s autopkgtest [19:38:44]: rebooting testbed after setup commands that affected boot
136s autopkgtest [19:39:02]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025
139s autopkgtest [19:39:05]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled
140s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (dsc) [2141 B]
140s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (tar) [155 kB]
140s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-3build2 (diff) [6012 B]
140s gpgv: Signature made Tue Mar  4 16:32:02 2025 UTC
140s gpgv:                using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2
140s gpgv: Can't check signature: No public key
140s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-3build2.dsc: no acceptable signature found
141s autopkgtest [19:39:07]: testing package uncalled version 2.3+ds-3build2
141s autopkgtest [19:39:07]: build not needed
141s autopkgtest [19:39:07]: test run-unit-test: preparing testbed
142s Reading package lists...
142s Building dependency tree...
142s Reading state information...
142s Starting pkgProblemResolver with broken count: 0
142s Starting 2 pkgProblemResolver with broken count: 0
142s Done
142s The following NEW packages will be installed:
142s   libaec0 libblas3 libgfortran5 libhdf5-310 liblapack3 libsz2 python3-numpy
142s   python3-numpy-dev uncalled
142s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
142s Need to get 10.5 MB of archives.
142s After this operation, 40.6 MB of additional disk space will be used.
142s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB]
143s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB]
143s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB]
143s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB]
143s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB]
144s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB]
144s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B]
144s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB]
144s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x uncalled s390x 2.3+ds-3build2 [651 kB]
144s Fetched 10.5 MB in 2s (6500 kB/s)
144s Selecting previously unselected package python3-numpy-dev:s390x.
144s (Reading database ... 
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(Reading database ... 56326 files and directories currently installed.)
144s Preparing to unpack .../0-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ...
144s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ...
144s Selecting previously unselected package libblas3:s390x.
144s Preparing to unpack .../1-libblas3_3.12.1-2_s390x.deb ...
144s Unpacking libblas3:s390x (3.12.1-2) ...
144s Selecting previously unselected package libgfortran5:s390x.
144s Preparing to unpack .../2-libgfortran5_15-20250222-0ubuntu1_s390x.deb ...
144s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ...
144s Selecting previously unselected package liblapack3:s390x.
144s Preparing to unpack .../3-liblapack3_3.12.1-2_s390x.deb ...
144s Unpacking liblapack3:s390x (3.12.1-2) ...
144s Selecting previously unselected package python3-numpy.
144s Preparing to unpack .../4-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ...
144s Unpacking python3-numpy (1:2.2.3+ds-5) ...
144s Selecting previously unselected package libaec0:s390x.
144s Preparing to unpack .../5-libaec0_1.1.3-1_s390x.deb ...
144s Unpacking libaec0:s390x (1.1.3-1) ...
144s Selecting previously unselected package libsz2:s390x.
144s Preparing to unpack .../6-libsz2_1.1.3-1_s390x.deb ...
144s Unpacking libsz2:s390x (1.1.3-1) ...
144s Selecting previously unselected package libhdf5-310:s390x.
144s Preparing to unpack .../7-libhdf5-310_1.14.5+repack-3_s390x.deb ...
144s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ...
144s Selecting previously unselected package uncalled.
144s Preparing to unpack .../8-uncalled_2.3+ds-3build2_s390x.deb ...
144s Unpacking uncalled (2.3+ds-3build2) ...
144s Setting up libaec0:s390x (1.1.3-1) ...
144s Setting up libblas3:s390x (3.12.1-2) ...
144s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
144s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ...
144s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ...
144s Setting up libsz2:s390x (1.1.3-1) ...
144s Setting up liblapack3:s390x (3.12.1-2) ...
144s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
144s Setting up python3-numpy (1:2.2.3+ds-5) ...
146s Setting up libhdf5-310:s390x (1.14.5+repack-3) ...
146s Setting up uncalled (2.3+ds-3build2) ...
146s Processing triggers for libc-bin (2.41-1ubuntu2) ...
146s Processing triggers for man-db (2.13.0-1) ...
147s autopkgtest [19:39:13]: test run-unit-test: [-----------------------
147s [bwa_index] Pack FASTA... 0.00 sec
147s [bwa_index] Construct BWT for the packed sequence...
147s [bwa_index] 0.00 seconds elapse.
147s [bwa_index] Update BWT... 0.00 sec
147s [bwa_index] Pack forward-only FASTA... 0.00 sec
147s [bwa_index] Construct SA from BWT and Occ... 0.00 sec
147s Initializing parameter search
147s Computing default parameters
147s Writing default parameters
147s Done
148s Loading fast5s
148s Mapping
148s Finishing
148s f41a60f7-de4a-4b17-9f54-387e52d60b65	106	73	106	-	Escherichia_coli_chromosome:2400000-2410000	10000	6938	6976	38	39	255	ch:i:486	st:i:257117	mt:f:9.604129
148s autopkgtest [19:39:14]: test run-unit-test: -----------------------]
148s run-unit-test        PASS
148s autopkgtest [19:39:14]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
149s autopkgtest [19:39:15]: @@@@@@@@@@@@@@@@@@@@ summary
149s run-unit-test        PASS
154s nova [W] Using flock in prodstack6-s390x
154s flock: timeout while waiting to get lock
154s Creating nova instance adt-plucky-s390x-uncalled-20250315-193645-juju-7f2275-prod-proposed-migration-environment-2-499559dd-364e-48fd-8334-fb8196b0e427 from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)...
154s nova [W] Timed out waiting for 2eccff26-e303-4fcd-af5d-a5e861592df0 to get deleted.