0s autopkgtest [19:37:06]: starting date and time: 2024-11-14 19:37:06+0000 0s autopkgtest [19:37:06]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [19:37:06]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.06xx0l99/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.76 lxd-armhf-10.145.243.76:autopkgtest/ubuntu/plucky/armhf 53s autopkgtest [19:37:59]: testbed dpkg architecture: armhf 55s autopkgtest [19:38:01]: testbed apt version: 2.9.8 55s autopkgtest [19:38:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [110 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [674 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4136 B] 64s Fetched 1926 kB in 1s (1877 kB/s) 64s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 102s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 102s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 102s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 102s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 105s Reading package lists... 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade... 106s The following packages will be upgraded: 106s libcap-ng0 pastebinit python3-systemd 106s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s Need to get 72.8 kB of archives. 106s After this operation, 89.1 kB of additional disk space will be used. 106s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf libcap-ng0 armhf 0.8.5-3build1 [13.8 kB] 107s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pastebinit all 1.7.1-1 [14.9 kB] 107s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-systemd armhf 235-1build5 [44.0 kB] 107s Fetched 72.8 kB in 0s (212 kB/s) 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 ... 59560 files and directories currently installed.) 107s Preparing to unpack .../libcap-ng0_0.8.5-3build1_armhf.deb ... 107s Unpacking libcap-ng0:armhf (0.8.5-3build1) over (0.8.5-1) ... 107s Setting up libcap-ng0:armhf (0.8.5-3build1) ... 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 ... 59560 files and directories currently installed.) 107s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 107s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 107s Preparing to unpack .../python3-systemd_235-1build5_armhf.deb ... 108s Unpacking python3-systemd (235-1build5) over (235-1build4) ... 108s Setting up pastebinit (1.7.1-1) ... 108s Setting up python3-systemd (235-1build5) ... 108s Processing triggers for man-db (2.12.1-3) ... 109s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 111s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 113s autopkgtest [19:38:59]: rebooting testbed after setup commands that affected boot 182s autopkgtest [19:40:08]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 209s autopkgtest [19:40:35]: @@@@@@@@@@@@@@@@@@@@ apt-source uncalled 219s Get:1 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (dsc) [2117 B] 219s Get:2 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (tar) [155 kB] 219s Get:3 http://ftpmaster.internal/ubuntu plucky/universe uncalled 2.3+ds-2 (diff) [5072 B] 219s gpgv: Signature made Wed Aug 21 15:42:41 2024 UTC 219s gpgv: using RSA key 33CB284313E90BD27DCB4523600316A6DC277476 219s gpgv: Can't check signature: No public key 219s dpkg-source: warning: cannot verify inline signature for ./uncalled_2.3+ds-2.dsc: no acceptable signature found 219s autopkgtest [19:40:45]: testing package uncalled version 2.3+ds-2 221s autopkgtest [19:40:47]: build not needed 223s autopkgtest [19:40:49]: test run-unit-test: preparing testbed 233s Reading package lists... 234s Building dependency tree... 234s Reading state information... 234s Starting pkgProblemResolver with broken count: 0 235s Starting 2 pkgProblemResolver with broken count: 0 235s Done 237s The following additional packages will be installed: 237s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 libsz2 237s python3-numpy uncalled 237s Suggested packages: 237s gcc gfortran python-numpy-doc python3-dev python3-pytest 237s The following NEW packages will be installed: 237s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 liblapack3 237s libsz2 python3-numpy uncalled 237s 0 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. 237s Need to get 8461 kB/8462 kB of archives. 237s After this operation, 31.7 MB of additional disk space will be used. 237s Get:1 /tmp/autopkgtest.4r3At9/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [708 B] 237s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 237s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 237s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 237s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 237s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 237s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 237s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 238s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf uncalled armhf 2.3+ds-2 [611 kB] 238s Fetched 8461 kB in 1s (9959 kB/s) 238s Selecting previously unselected package libaec0:armhf. 238s (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 ... 59565 files and directories currently installed.) 238s Preparing to unpack .../0-libaec0_1.1.3-1_armhf.deb ... 238s Unpacking libaec0:armhf (1.1.3-1) ... 238s Selecting previously unselected package libblas3:armhf. 238s Preparing to unpack .../1-libblas3_3.12.0-3build2_armhf.deb ... 238s Unpacking libblas3:armhf (3.12.0-3build2) ... 238s Selecting previously unselected package libgfortran5:armhf. 238s Preparing to unpack .../2-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 238s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 238s Selecting previously unselected package libsz2:armhf. 238s Preparing to unpack .../3-libsz2_1.1.3-1_armhf.deb ... 238s Unpacking libsz2:armhf (1.1.3-1) ... 238s Selecting previously unselected package libhdf5-103-1t64:armhf. 238s Preparing to unpack .../4-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 238s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 238s Selecting previously unselected package liblapack3:armhf. 239s Preparing to unpack .../5-liblapack3_3.12.0-3build2_armhf.deb ... 239s Unpacking liblapack3:armhf (3.12.0-3build2) ... 239s Selecting previously unselected package python3-numpy. 239s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 239s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 239s Selecting previously unselected package uncalled. 239s Preparing to unpack .../7-uncalled_2.3+ds-2_armhf.deb ... 239s Unpacking uncalled (2.3+ds-2) ... 239s Selecting previously unselected package autopkgtest-satdep. 239s Preparing to unpack .../8-1-autopkgtest-satdep.deb ... 239s Unpacking autopkgtest-satdep (0) ... 239s Setting up libaec0:armhf (1.1.3-1) ... 239s Setting up libblas3:armhf (3.12.0-3build2) ... 239s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 239s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 239s Setting up libsz2:armhf (1.1.3-1) ... 239s Setting up liblapack3:armhf (3.12.0-3build2) ... 239s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 239s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 242s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 242s Setting up uncalled (2.3+ds-2) ... 242s /usr/lib/python3/dist-packages/uncalled/debug.py:23: SyntaxWarning: invalid escape sequence '\d' 242s CIG_RE = re.compile("(\d+)(["+CIG_OPS_STR+"])") 242s Setting up autopkgtest-satdep (0) ... 242s Processing triggers for man-db (2.12.1-3) ... 242s Processing triggers for libc-bin (2.40-1ubuntu3) ... 254s (Reading database ... 60546 files and directories currently installed.) 254s Removing autopkgtest-satdep (0) ... 260s autopkgtest [19:41:26]: test run-unit-test: [----------------------- 262s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 262s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 262s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 262s port_re = re.compile("grpc_port = (\d+)") 262s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 262s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 262s [bwa_index] Pack FASTA... 0.00 sec 262s [bwa_index] Construct BWT for the packed sequence... 262s [bwa_index] 0.00 seconds elapse. 262s [bwa_index] Update BWT... 0.00 sec 262s [bwa_index] Pack forward-only FASTA... 0.00 sec 262s [bwa_index] Construct SA from BWT and Occ... 0.00 sec 262s Initializing parameter search 262s Computing default parameters 262s Writing default parameters 262s Done 262s /usr/bin/uncalled:307: SyntaxWarning: invalid escape sequence '\-' 262s log_re = re.compile("^([0-9\-]+ [0-9:]+).+ :.+instance_started.+") 262s /usr/bin/uncalled:308: SyntaxWarning: invalid escape sequence '\d' 262s port_re = re.compile("grpc_port = (\d+)") 262s /usr/bin/uncalled:309: SyntaxWarning: invalid escape sequence '\s' 262s device_re = re.compile("(device_id|instance) = ([^\s,]+)") 263s Loading fast5s 263s Mapping 263s Finishing 263s 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:14.155888 263s autopkgtest [19:41:29]: test run-unit-test: -----------------------] 267s autopkgtest [19:41:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 267s run-unit-test PASS 271s autopkgtest [19:41:37]: @@@@@@@@@@@@@@@@@@@@ summary 271s run-unit-test PASS