0s autopkgtest [16:59:13]: starting date and time: 2024-11-14 16:59:13+0000 0s autopkgtest [16:59:13]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:59:13]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.anbno21r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade uncalled --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-11.secgroup --name adt-plucky-s390x-uncalled-20241114-165913-juju-7f2275-prod-proposed-migration-environment-20-45bbfe58-0189-457c-a186-5fe214c629dc --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/ 100s autopkgtest [17:00:53]: testbed dpkg architecture: s390x 100s autopkgtest [17:00:53]: testbed apt version: 2.9.8 100s autopkgtest [17:00:53]: @@@@@@@@@@@@@@@@@@@@ test bed setup 101s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 101s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 101s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 101s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 101s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [117 kB] 101s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [674 kB] 101s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [5020 B] 101s Fetched 1947 kB in 1s (2548 kB/s) 101s Reading package lists... 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Calculating upgrade... 104s The following packages will be upgraded: 104s libcap-ng0 pastebinit python3-systemd 104s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Need to get 77.8 kB of archives. 104s After this operation, 123 kB of additional disk space will be used. 104s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x libcap-ng0 s390x 0.8.5-3build1 [15.9 kB] 104s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pastebinit all 1.7.1-1 [14.9 kB] 104s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-systemd s390x 235-1build5 [46.9 kB] 104s Fetched 77.8 kB in 0s (230 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 ... 55511 files and directories currently installed.) 104s Preparing to unpack .../libcap-ng0_0.8.5-3build1_s390x.deb ... 104s Unpacking libcap-ng0:s390x (0.8.5-3build1) over (0.8.5-1) ... 104s Setting up libcap-ng0:s390x (0.8.5-3build1) ... 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 ... 55511 files and directories currently installed.) 104s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 104s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 104s Preparing to unpack .../python3-systemd_235-1build5_s390x.deb ... 105s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 105s Setting up pastebinit (1.7.1-1) ... 105s Setting up python3-systemd (235-1build5) ... 105s 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... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s 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 107s Reading package lists... 107s 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... 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 110s autopkgtest [17:01:03]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 110s autopkgtest [17:01:03]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 112s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 112s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 112s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 112s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 112s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 112s gpgv: Can't check signature: No public key 112s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 112s autopkgtest [17:01:05]: testing package uncalled version 2.3+ds-2 112s autopkgtest [17:01:05]: build not needed 113s autopkgtest [17:01:06]: test run-unit-test: preparing testbed 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Starting pkgProblemResolver with broken count: 0 114s Starting 2 pkgProblemResolver with broken count: 0 114s Done 115s The following additional packages will be installed: 115s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 115s python3-numpy uncalled 115s Suggested packages: 115s gcc gfortran python-numpy-doc python3-dev python3-pytest 115s The following NEW packages will be installed: 115s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 115s libsz2 python3-numpy uncalled 115s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 10.5 MB/10.5 MB of archives. 115s After this operation, 48.5 MB of additional disk space will be used. 115s Get:1 /tmp/autopkgtest.YZAjX6/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [708 B] 115s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 115s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 115s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 115s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 115s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x uncalled s390x 2.3+ds-2 [650 kB] 116s Fetched 10.5 MB in 1s (12.0 MB/s) 116s Selecting previously unselected package libaec0:s390x. 116s (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 ... 55516 files and directories currently installed.) 116s Preparing to unpack .../0-libaec0_1.1.3-1_s390x.deb ... 116s Unpacking libaec0:s390x (1.1.3-1) ... 116s Selecting previously unselected package libblas3:s390x. 116s Preparing to unpack .../1-libblas3_3.12.0-3build2_s390x.deb ... 116s Unpacking libblas3:s390x (3.12.0-3build2) ... 116s Selecting previously unselected package libgfortran5:s390x. 116s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 116s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 116s Selecting previously unselected package libsz2:s390x. 116s Preparing to unpack .../3-libsz2_1.1.3-1_s390x.deb ... 116s Unpacking libsz2:s390x (1.1.3-1) ... 116s Selecting previously unselected package libhdf5-103-1t64:s390x. 116s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 116s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 116s Selecting previously unselected package liblapack3:s390x. 116s Preparing to unpack .../5-liblapack3_3.12.0-3build2_s390x.deb ... 116s Unpacking liblapack3:s390x (3.12.0-3build2) ... 116s Selecting previously unselected package python3-numpy. 116s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11ubuntu1_s390x.deb ... 116s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 116s Selecting previously unselected package uncalled. 116s Preparing to unpack .../7-uncalled_2.3+ds-2_s390x.deb ... 116s Unpacking uncalled (2.3+ds-2) ... 116s Selecting previously unselected package autopkgtest-satdep. 116s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 116s Unpacking autopkgtest-satdep (0) ... 116s Setting up libaec0:s390x (1.1.3-1) ... 116s Setting up libblas3:s390x (3.12.0-3build2) ... 116s 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 116s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 116s Setting up libsz2:s390x (1.1.3-1) ... 116s Setting up liblapack3:s390x (3.12.0-3build2) ... 116s 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 116s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 118s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 118s Setting up uncalled (2.3+ds-2) ... 118s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 118s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 118s Setting up autopkgtest-satdep (0) ... 118s Processing triggers for man-db (2.12.1-3) ... 118s Processing triggers for libc-bin (2.40-1ubuntu3) ... 120s (Reading database ... 56496 files and directories currently installed.) 120s Removing autopkgtest-satdep (0) ... 121s autopkgtest [17:01:14]: test run-unit-test: [----------------------- 121s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 121s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 121s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 121s port_re = re.compile("grpc_port = (\d+)") 121s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 121s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 121s [bwa_index] Pack FASTA... 0.00 sec 121s [bwa_index] Construct BWT for the packed sequence... 121s [bwa_index] 0.00 seconds elapse. 121s [bwa_index] Update BWT... 0.00 sec 121s [bwa_index] Pack forward-only FASTA... 0.00 sec 121s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 121s Initializing parameter search 121s Computing default parameters 121s Writing default parameters 121s Done 121s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 121s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 121s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 121s port_re = re.compile("grpc_port = (\d+)") 121s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 121s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 121s Loading fast5s 121s Mapping 121s Finishing 121s 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:9.312864 122s autopkgtest [17:01:15]: test run-unit-test: -----------------------] 122s autopkgtest [17:01:15]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 122s run-unit-test PASS 122s autopkgtest [17:01:15]: @@@@@@@@@@@@@@@@@@@@ summary 122s run-unit-test PASS 135s nova [W] Using flock in prodstack6-s390x 135s Creating nova instance adt-plucky-s390x-uncalled-20241114-165913-juju-7f2275-prod-proposed-migration-environment-20-45bbfe58-0189-457c-a186-5fe214c629dc from image adt/ubuntu-plucky-s390x-server-20241114.img (UUID 41a907ef-1f3c-4685-a0eb-228b0d61c6b5)...