0s autopkgtest [16:49:02]: starting date and time: 2024-11-14 16:49:02+0000 0s autopkgtest [16:49:02]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:49:02]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.v1_oekmr/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-31.secgroup --name adt-plucky-arm64-uncalled-20241114-164902-juju-7f2275-prod-proposed-migration-environment-15-a913dabf-9339-4e9e-837f-ce1d507c2fc7 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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,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/ 76s autopkgtest [16:50:17]: testbed dpkg architecture: arm64 76s autopkgtest [16:50:17]: testbed apt version: 2.9.8 76s autopkgtest [16:50:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 77s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 77s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [951 kB] 77s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.6 kB] 77s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [136 kB] 77s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 77s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [711 kB] 77s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [5488 B] 77s Fetched 2054 kB in 1s (1973 kB/s) 77s Reading package lists... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 83s The following packages will be upgraded: 83s libcap-ng0 pastebinit python3-systemd 83s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Need to get 76.6 kB of archives. 83s After this operation, 349 kB of additional disk space will be used. 83s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 libcap-ng0 arm64 0.8.5-3build1 [15.0 kB] 83s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 pastebinit all 1.7.1-1 [14.9 kB] 83s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-systemd arm64 235-1build5 [46.7 kB] 84s Fetched 76.6 kB in 0s (220 kB/s) 84s (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 ... 79925 files and directories currently installed.) 84s Preparing to unpack .../libcap-ng0_0.8.5-3build1_arm64.deb ... 84s Unpacking libcap-ng0:arm64 (0.8.5-3build1) over (0.8.5-1) ... 84s Setting up libcap-ng0:arm64 (0.8.5-3build1) ... 84s (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 ... 79925 files and directories currently installed.) 84s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 84s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 84s Preparing to unpack .../python3-systemd_235-1build5_arm64.deb ... 84s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 84s Setting up pastebinit (1.7.1-1) ... 84s Setting up python3-systemd (235-1build5) ... 85s Processing triggers for man-db (2.12.1-3) ... 85s Processing triggers for libc-bin (2.40-1ubuntu3) ... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 88s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 88s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 88s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 90s Reading package lists... 90s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s Calculating upgrade... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 98s autopkgtest [16:50:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 98s autopkgtest [16:50:40]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 100s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 100s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 100s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 100s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 100s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 100s gpgv: Can't check signature: No public key 100s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 100s autopkgtest [16:50:42]: testing package uncalled version 2.3+ds-2 101s autopkgtest [16:50:43]: build not needed 101s autopkgtest [16:50:43]: test run-unit-test: preparing testbed 103s Reading package lists... 103s Building dependency tree... 103s Reading state information... 104s Starting pkgProblemResolver with broken count: 0 104s Starting 2 pkgProblemResolver with broken count: 0 104s Done 105s The following additional packages will be installed: 105s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 105s python3-numpy uncalled 105s Suggested packages: 105s gcc gfortran python-numpy-doc python3-dev python3-pytest 106s The following NEW packages will be installed: 106s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 106s libsz2 python3-numpy uncalled 106s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 8840 kB/8841 kB of archives. 106s After this operation, 41.4 MB of additional disk space will be used. 106s Get:1 /tmp/autopkgtest.FgDAgb/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [704 B] 106s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 106s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 106s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 106s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 106s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 106s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 106s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 106s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 uncalled arm64 2.3+ds-2 [574 kB] 107s Fetched 8840 kB in 1s (8984 kB/s) 107s Selecting previously unselected package libaec0:arm64. 107s (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 ... 79930 files and directories currently installed.) 107s Preparing to unpack .../0-libaec0_1.1.3-1_arm64.deb ... 107s Unpacking libaec0:arm64 (1.1.3-1) ... 107s Selecting previously unselected package libblas3:arm64. 107s Preparing to unpack .../1-libblas3_3.12.0-3build2_arm64.deb ... 107s Unpacking libblas3:arm64 (3.12.0-3build2) ... 107s Selecting previously unselected package libgfortran5:arm64. 107s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 107s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 107s Selecting previously unselected package libsz2:arm64. 107s Preparing to unpack .../3-libsz2_1.1.3-1_arm64.deb ... 107s Unpacking libsz2:arm64 (1.1.3-1) ... 108s Selecting previously unselected package libhdf5-103-1t64:arm64. 108s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 108s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 108s Selecting previously unselected package liblapack3:arm64. 108s Preparing to unpack .../5-liblapack3_3.12.0-3build2_arm64.deb ... 108s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 108s Selecting previously unselected package python3-numpy. 108s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 108s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 108s Selecting previously unselected package uncalled. 108s Preparing to unpack .../7-uncalled_2.3+ds-2_arm64.deb ... 108s Unpacking uncalled (2.3+ds-2) ... 108s Selecting previously unselected package autopkgtest-satdep. 108s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 108s Unpacking autopkgtest-satdep (0) ... 108s Setting up libaec0:arm64 (1.1.3-1) ... 108s Setting up libblas3:arm64 (3.12.0-3build2) ... 108s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 108s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 108s Setting up libsz2:arm64 (1.1.3-1) ... 108s Setting up liblapack3:arm64 (3.12.0-3build2) ... 108s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 108s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 111s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 111s Setting up uncalled (2.3+ds-2) ... 111s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 111s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 111s Setting up autopkgtest-satdep (0) ... 111s Processing triggers for man-db (2.12.1-3) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s (Reading database ... 80910 files and directories currently installed.) 116s Removing autopkgtest-satdep (0) ... 117s autopkgtest [16:50:59]: test run-unit-test: [----------------------- 117s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 117s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 117s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 117s port_re = re.compile("grpc_port = (\d+)") 117s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 117s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 117s [bwa_index] Pack FASTA... 0.00 sec 117s [bwa_index] Construct BWT for the packed sequence... 117s [bwa_index] 0.00 seconds elapse. 117s [bwa_index] Update BWT... 0.00 sec 117s [bwa_index] Pack forward-only FASTA... 0.00 sec 117s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 117s Initializing parameter search 118s Computing default parameters 118s Writing default parameters 118s Done 118s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 118s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 118s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 118s port_re = re.compile("grpc_port = (\d+)") 118s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 118s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 118s Loading fast5s 118s Mapping 118s Finishing 118s 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:9.055397 119s autopkgtest [16:51:01]: test run-unit-test: -----------------------] 119s autopkgtest [16:51:01]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 119s run-unit-test PASS 120s autopkgtest [16:51:02]: @@@@@@@@@@@@@@@@@@@@ summary 120s run-unit-test PASS 133s nova [W] Skipping flock in bos03-arm64 133s Creating nova instance adt-plucky-arm64-uncalled-20241114-164902-juju-7f2275-prod-proposed-migration-environment-15-a913dabf-9339-4e9e-837f-ce1d507c2fc7 from image adt/ubuntu-plucky-arm64-server-20241114.img (UUID 4472f5f7-859f-4441-9e8e-9550fb35f210)...