0s autopkgtest [16:53:21]: starting date and time: 2024-11-13 16:53:21+0000 0s autopkgtest [16:53:21]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:53:21]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.m5_noyz_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-7.secgroup --name adt-plucky-s390x-uncalled-20241113-165321-juju-7f2275-prod-proposed-migration-environment-20-d68a15d4-62c2-4d29-a03e-97ed90b68192 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 98s autopkgtest [16:54:59]: testbed dpkg architecture: s390x 99s autopkgtest [16:55:00]: testbed apt version: 2.9.8 99s autopkgtest [16:55:00]: @@@@@@@@@@@@@@@@@@@@ test bed setup 99s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 100s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [971 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 100s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 100s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 100s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [112 kB] 100s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [646 kB] 100s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.8 kB] 100s Fetched 1949 kB in 1s (2223 kB/s) 100s Reading package lists... 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s Calculating upgrade... 103s The following NEW packages will be installed: 103s python3.13-gdbm 103s The following packages will be upgraded: 103s libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common 103s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 103s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 1285 kB of archives. 103s After this operation, 103 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 103s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 103s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 103s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B] 103s Fetched 1285 kB in 1s (2299 kB/s) 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (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 ... 55510 files and directories currently installed.) 104s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 104s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 104s Setting up python3-minimal (3.12.7-1) ... 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (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 ... 55510 files and directories currently installed.) 104s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 104s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 104s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 104s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 104s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ... 104s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 104s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ... 104s Selecting previously unselected package python3.13-gdbm. 104s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (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 ... 55510 files and directories currently installed.) 104s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ... 104s Unpacking python3.13-gdbm (3.13.0-2) ... 104s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ... 104s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 104s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 104s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 104s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 104s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 104s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ... 104s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ... 104s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ... 104s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ... 104s Setting up libutempter0:s390x (1.2.1-4) ... 104s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 104s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 104s Setting up python3.13-gdbm (3.13.0-2) ... 104s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 104s Setting up python3 (3.12.7-1) ... 104s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ... 104s Setting up python3-gdbm:s390x (3.12.7-1) ... 104s Processing triggers for man-db (2.12.1-3) ... 105s Processing triggers for libc-bin (2.40-1ubuntu3) ... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 106s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 106s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 106s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s Calculating upgrade... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [16:55:11]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 110s autopkgtest [16:55:11]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 111s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 111s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 111s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 111s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 111s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 111s gpgv: Can't check signature: No public key 111s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 111s autopkgtest [16:55:12]: testing package uncalled version 2.3+ds-2 112s autopkgtest [16:55:13]: build not needed 112s autopkgtest [16:55:13]: test run-unit-test: preparing testbed 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s The following additional packages will be installed: 114s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 114s python3-numpy uncalled 114s Suggested packages: 114s gcc gfortran python-numpy-doc python3-dev python3-pytest 114s The following NEW packages will be installed: 114s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 114s libsz2 python3-numpy uncalled 114s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 9998 kB/9998 kB of archives. 114s After this operation, 38.4 MB of additional disk space will be used. 114s Get:1 /tmp/autopkgtest.1gguUD/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 114s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 114s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 114s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 114s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 114s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x uncalled s390x 2.3+ds-2 [650 kB] 115s Fetched 9998 kB in 1s (11.5 MB/s) 115s Selecting previously unselected package libaec0:s390x. 115s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (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 ... 55517 files and directories currently installed.) 115s Preparing to unpack .../0-libaec0_1.1.3-1_s390x.deb ... 115s Unpacking libaec0:s390x (1.1.3-1) ... 115s Selecting previously unselected package libblas3:s390x. 115s Preparing to unpack .../1-libblas3_3.12.0-3build2_s390x.deb ... 115s Unpacking libblas3:s390x (3.12.0-3build2) ... 115s Selecting previously unselected package libgfortran5:s390x. 115s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 115s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 115s Selecting previously unselected package libsz2:s390x. 115s Preparing to unpack .../3-libsz2_1.1.3-1_s390x.deb ... 115s Unpacking libsz2:s390x (1.1.3-1) ... 115s Selecting previously unselected package libhdf5-103-1t64:s390x. 115s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 115s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 115s Selecting previously unselected package liblapack3:s390x. 115s Preparing to unpack .../5-liblapack3_3.12.0-3build2_s390x.deb ... 115s Unpacking liblapack3:s390x (3.12.0-3build2) ... 115s Selecting previously unselected package python3-numpy. 115s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 115s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 115s Selecting previously unselected package uncalled. 115s Preparing to unpack .../7-uncalled_2.3+ds-2_s390x.deb ... 115s Unpacking uncalled (2.3+ds-2) ... 115s Selecting previously unselected package autopkgtest-satdep. 115s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 115s Unpacking autopkgtest-satdep (0) ... 115s Setting up libaec0:s390x (1.1.3-1) ... 115s Setting up libblas3:s390x (3.12.0-3build2) ... 115s 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 115s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 115s Setting up libsz2:s390x (1.1.3-1) ... 115s Setting up liblapack3:s390x (3.12.0-3build2) ... 115s 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 115s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 117s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 117s Setting up uncalled (2.3+ds-2) ... 117s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 117s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 117s Setting up autopkgtest-satdep (0) ... 117s Processing triggers for man-db (2.12.1-3) ... 117s Processing triggers for libc-bin (2.40-1ubuntu3) ... 119s (Reading database ... 56477 files and directories currently installed.) 119s Removing autopkgtest-satdep (0) ... 120s autopkgtest [16:55:21]: test run-unit-test: [----------------------- 120s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 120s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 120s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 120s port_re = re.compile("grpc_port = (\d+)") 120s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 120s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 120s [bwa_index] Pack FASTA... 0.00 sec 120s [bwa_index] Construct BWT for the packed sequence... 120s [bwa_index] 0.00 seconds elapse. 120s [bwa_index] Update BWT... 0.00 sec 120s [bwa_index] Pack forward-only FASTA... 0.00 sec 120s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 120s Initializing parameter search 120s Computing default parameters 120s Writing default parameters 120s Done 120s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 120s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 120s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 120s port_re = re.compile("grpc_port = (\d+)") 120s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 120s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 120s Loading fast5s 120s Mapping 120s Finishing 120s 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:9.303807 121s autopkgtest [16:55:22]: test run-unit-test: -----------------------] 121s autopkgtest [16:55:22]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 121s run-unit-test PASS 121s autopkgtest [16:55:22]: @@@@@@@@@@@@@@@@@@@@ summary 121s run-unit-test PASS 133s nova [W] Using flock in prodstack6-s390x 133s flock: timeout while waiting to get lock 133s Creating nova instance adt-plucky-s390x-uncalled-20241113-165321-juju-7f2275-prod-proposed-migration-environment-20-d68a15d4-62c2-4d29-a03e-97ed90b68192 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...