0s autopkgtest [09:51:09]: starting date and time: 2024-11-13 09:51:09+0000 0s autopkgtest [09:51:09]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [09:51:09]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.e7atjufd/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 picopore --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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-47.secgroup --name adt-plucky-arm64-picopore-20241113-095109-juju-7f2275-prod-proposed-migration-environment-15-ec114827-fa4b-4829-84b0-f43888ac5342 --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/ 78s autopkgtest [09:52:27]: testbed dpkg architecture: arm64 80s autopkgtest [09:52:27]: testbed apt version: 2.9.8 80s autopkgtest [09:52:27]: @@@@@@@@@@@@@@@@@@@@ test bed setup 80s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 80s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 80s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 80s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 80s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 80s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 80s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 80s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 80s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 80s Fetched 1794 kB in 1s (1798 kB/s) 80s Reading package lists... 83s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 86s The following NEW packages will be installed: 86s python3.13-gdbm 86s The following packages will be upgraded: 86s libpython3-stdlib python3 python3-gdbm python3-minimal 86s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 86s Need to get 101 kB of archives. 86s After this operation, 141 kB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 86s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 86s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 87s Fetched 101 kB in 0s (281 kB/s) 87s (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 ... 79924 files and directories currently installed.) 87s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 87s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 87s Setting up python3-minimal (3.12.7-1) ... 87s (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 ... 79924 files and directories currently installed.) 87s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 87s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 88s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 88s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 88s Selecting previously unselected package python3.13-gdbm. 88s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 88s Unpacking python3.13-gdbm (3.13.0-2) ... 88s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 88s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 88s Setting up python3.13-gdbm (3.13.0-2) ... 88s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 88s Setting up python3 (3.12.7-1) ... 88s Setting up python3-gdbm:arm64 (3.12.7-1) ... 88s Processing triggers for man-db (2.12.1-3) ... 89s Reading package lists... 90s Building dependency tree... 90s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 94s Reading package lists... 94s Reading package lists... 95s Building dependency tree... 95s Reading state information... 96s Calculating upgrade... 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 98s Building dependency tree... 98s Reading state information... 98s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s autopkgtest [09:52:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 102s autopkgtest [09:52:51]: @@@@@@@@@@@@@@@@@@@@ apt-source picopore 105s Get:1 http://ftpmaster.internal/ubuntu plucky/universe picopore 1.2.0-3 (dsc) [2191 B] 105s Get:2 http://ftpmaster.internal/ubuntu plucky/universe picopore 1.2.0-3 (tar) [6276 kB] 105s Get:3 http://ftpmaster.internal/ubuntu plucky/universe picopore 1.2.0-3 (diff) [5332 B] 105s gpgv: Signature made Fri Dec 15 20:40:34 2023 UTC 105s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 105s gpgv: issuer "tille@debian.org" 105s gpgv: Can't check signature: No public key 105s dpkg-source: warning: cannot verify inline signature for ./picopore_1.2.0-3.dsc: no acceptable signature found 106s autopkgtest [09:52:55]: testing package picopore version 1.2.0-3 106s autopkgtest [09:52:55]: build not needed 107s autopkgtest [09:52:56]: test run-unit-test: preparing testbed 110s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 112s Starting 2 pkgProblemResolver with broken count: 0 112s Done 113s The following additional packages will be installed: 113s hdf5-tools libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 113s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblzf1 113s libpython3.13-minimal libpython3.13-stdlib libsz2 picopore python3-all 113s python3-h5py python3-h5py-serial python3-numpy python3-picopore 113s python3-watchdog python3.13 python3.13-minimal 113s Suggested packages: 113s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 113s python3.13-venv python3.13-doc binfmt-support 113s Recommended packages: 113s javascript-common 113s The following NEW packages will be installed: 113s autopkgtest-satdep hdf5-tools libaec0 libblas3 libgfortran5 libhdf5-103-1t64 113s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 113s liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2 picopore 113s python3-all python3-h5py python3-h5py-serial python3-numpy python3-picopore 113s python3-watchdog python3.13 python3.13-minimal 113s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 15.7 MB/15.8 MB of archives. 113s After this operation, 66.0 MB of additional disk space will be used. 113s Get:1 /tmp/autopkgtest.9TJtjC/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 115s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 115s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 hdf5-tools arm64 1.10.10+repack-4ubuntu3 [319 kB] 115s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 116s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 116s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 116s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 116s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 116s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 116s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 116s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 116s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 117s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 118s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 118s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 118s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-watchdog all 5.0.0-1 [125 kB] 118s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-picopore all 1.2.0-3 [15.6 kB] 118s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 picopore all 1.2.0-3 [9878 B] 118s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 119s Get:24 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 119s Fetched 15.7 MB in 6s (2746 kB/s) 119s Selecting previously unselected package libpython3.13-minimal:arm64. 119s (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 ... 79931 files and directories currently installed.) 119s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 119s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 119s Selecting previously unselected package python3.13-minimal. 119s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 119s Unpacking python3.13-minimal (3.13.0-2) ... 119s Selecting previously unselected package libaec0:arm64. 119s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 119s Unpacking libaec0:arm64 (1.1.3-1) ... 119s Selecting previously unselected package libsz2:arm64. 119s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 119s Unpacking libsz2:arm64 (1.1.3-1) ... 120s Selecting previously unselected package libhdf5-103-1t64:arm64. 120s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 120s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 120s Selecting previously unselected package hdf5-tools. 120s Preparing to unpack .../05-hdf5-tools_1.10.10+repack-4ubuntu3_arm64.deb ... 120s Unpacking hdf5-tools (1.10.10+repack-4ubuntu3) ... 120s Selecting previously unselected package libblas3:arm64. 120s Preparing to unpack .../06-libblas3_3.12.0-3build2_arm64.deb ... 120s Unpacking libblas3:arm64 (3.12.0-3build2) ... 120s Selecting previously unselected package libgfortran5:arm64. 120s Preparing to unpack .../07-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 120s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 120s Selecting previously unselected package libhdf5-hl-100t64:arm64. 120s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 120s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 120s Selecting previously unselected package libjs-jquery. 120s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 120s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 120s Selecting previously unselected package libjs-underscore. 120s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 120s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 120s Selecting previously unselected package libjs-sphinxdoc. 120s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 120s Unpacking libjs-sphinxdoc (7.4.7-4) ... 120s Selecting previously unselected package liblapack3:arm64. 120s Preparing to unpack .../12-liblapack3_3.12.0-3build2_arm64.deb ... 120s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 120s Selecting previously unselected package liblzf1:arm64. 120s Preparing to unpack .../13-liblzf1_3.6-4_arm64.deb ... 120s Unpacking liblzf1:arm64 (3.6-4) ... 120s Selecting previously unselected package libpython3.13-stdlib:arm64. 120s Preparing to unpack .../14-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 120s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 120s Selecting previously unselected package python3-numpy. 120s Preparing to unpack .../15-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 120s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 121s Selecting previously unselected package python3-h5py-serial. 121s Preparing to unpack .../16-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 121s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 121s Selecting previously unselected package python3-h5py. 121s Preparing to unpack .../17-python3-h5py_3.11.0-5ubuntu1_all.deb ... 121s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 121s Selecting previously unselected package python3-watchdog. 121s Preparing to unpack .../18-python3-watchdog_5.0.0-1_all.deb ... 121s Unpacking python3-watchdog (5.0.0-1) ... 121s Selecting previously unselected package python3-picopore. 121s Preparing to unpack .../19-python3-picopore_1.2.0-3_all.deb ... 121s Unpacking python3-picopore (1.2.0-3) ... 121s Selecting previously unselected package picopore. 121s Preparing to unpack .../20-picopore_1.2.0-3_all.deb ... 121s Unpacking picopore (1.2.0-3) ... 121s Selecting previously unselected package python3.13. 121s Preparing to unpack .../21-python3.13_3.13.0-2_arm64.deb ... 121s Unpacking python3.13 (3.13.0-2) ... 121s Selecting previously unselected package python3-all. 121s Preparing to unpack .../22-python3-all_3.12.7-1_arm64.deb ... 121s Unpacking python3-all (3.12.7-1) ... 121s Selecting previously unselected package autopkgtest-satdep. 121s Preparing to unpack .../23-1-autopkgtest-satdep.deb ... 121s Unpacking autopkgtest-satdep (0) ... 121s Setting up libaec0:arm64 (1.1.3-1) ... 121s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 121s Setting up libblas3:arm64 (3.12.0-3build2) ... 121s 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 121s Setting up liblzf1:arm64 (3.6-4) ... 121s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 121s Setting up python3.13-minimal (3.13.0-2) ... 123s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 123s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 123s Setting up libsz2:arm64 (1.1.3-1) ... 123s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 123s Setting up liblapack3:arm64 (3.12.0-3build2) ... 123s 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 123s Setting up python3.13 (3.13.0-2) ... 125s Setting up python3-all (3.12.7-1) ... 125s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 131s Setting up libjs-sphinxdoc (7.4.7-4) ... 131s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 131s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 131s Setting up python3-watchdog (5.0.0-1) ... 131s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 132s Setting up hdf5-tools (1.10.10+repack-4ubuntu3) ... 132s Setting up python3-h5py (3.11.0-5ubuntu1) ... 132s Setting up python3-picopore (1.2.0-3) ... 133s Setting up picopore (1.2.0-3) ... 133s Setting up autopkgtest-satdep (0) ... 133s Processing triggers for systemd (256.5-2ubuntu4) ... 133s Processing triggers for man-db (2.12.1-3) ... 133s Processing triggers for libc-bin (2.40-1ubuntu3) ... 140s (Reading database ... 81926 files and directories currently installed.) 140s Removing autopkgtest-satdep (0) ... 141s autopkgtest [09:53:30]: test run-unit-test: [----------------------- 142s Performing lossless compression on 1 files... 142s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 142s .Complete. 142s Original size: 673522 142s Compressed size: 673522 142s Performing lossless decompression on 1 files... 142s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 142s .Complete. 142s Compressed size: 673522 142s Reverted size: 1347044 142s Checking equivalence of /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/albacore_1d_original.fast5 (file 1) and /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 (file 2)... 143s Complete with 0 errors. 143s Performing lossless compression on 1 files... 143s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 143s .Complete. 143s Original size: 673522 143s Compressed size: 673522 144s Performing deep lossless compression on 1 files... 144s .Complete. 144s Original size: 673522 144s Compressed size: 629000 144s Performing deep lossless decompression on 1 files... 144s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 144s .Complete. 144s Compressed size: 629000 144s Reverted size: 1276128 144s Checking equivalence of /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/albacore_1d_original.fast5 (file 1) and /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.albacore_1d_original.fast5 (file 2)... 144s Complete with 0 errors. 145s Performing deep lossless compression on 1 files... 145s .Complete. 145s Original size: 673522 145s Compressed size: 629000 145s Performing raw compression with FASTQ and summary on 1 files... 146s .Complete. 146s Original size: 673522 146s Compressed size: 119182 146s Performing raw compression with summary and no FASTQ on 1 files... 146s .Complete. 146s Original size: 673522 146s Compressed size: 103635 147s Performing raw compression with FASTQ and no summary on 1 files... 147s .Complete. 147s Original size: 673522 147s Compressed size: 116766 147s Performing raw compression with no summary and no FASTQ on 1 files... 147s .Complete. 147s Original size: 673522 147s Compressed size: 98915 148s Performing raw compression with manual keyword Analyses on 1 files... 148s .Complete. 148s Original size: 673522 148s Compressed size: 98915 148s Performing lossless compression on 1 files... 148s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 148s .Complete. 148s Original size: 2003942 148s Compressed size: 2003942 148s Performing lossless decompression on 1 files... 148s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 148s .Complete. 148s Compressed size: 2003942 148s Reverted size: 4007884 148s Checking equivalence of /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/metrichor_2d_original.fast5 (file 1) and /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 (file 2)... 149s Complete with 0 errors. 149s Performing lossless compression on 1 files... 149s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 149s .Complete. 149s Original size: 2003942 149s Compressed size: 2003942 150s Performing deep lossless compression on 1 files... 150s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 150s .Complete. 150s Original size: 2003942 150s Compressed size: 2003942 150s Performing deep lossless decompression on 1 files... 150s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 150s .Complete. 150s Compressed size: 2003942 150s Reverted size: 4007884 150s Checking equivalence of /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/metrichor_2d_original.fast5 (file 1) and /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 (file 2)... 150s Complete with 0 errors. 151s Performing deep lossless compression on 1 files... 151s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/sample_data/picopore.test.metrichor_2d_original.fast5 151s .Complete. 151s Original size: 2003942 151s Compressed size: 2003942 152s Performing raw compression with FASTQ and summary on 1 files... 152s .Complete. 152s Original size: 2003942 152s Compressed size: 270517 152s Performing raw compression with summary and no FASTQ on 1 files... 152s .Complete. 152s Original size: 2003942 152s Compressed size: 232978 153s Performing raw compression with FASTQ and no summary on 1 files... 153s .Complete. 153s Original size: 2003942 153s Compressed size: 261197 153s Performing raw compression with no summary and no FASTQ on 1 files... 154s .Complete. 154s Original size: 2003942 154s Compressed size: 219602 154s Performing raw compression with manual keyword Analyses on 1 files... 154s .Complete. 154s Original size: 2003942 154s Compressed size: 219602 155s Performing real time lossless compression... 155s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 155s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 164s ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/albacore_1d_original.fast5 174s .ERROR: 'Dataset' object has no attribute 'value' on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 185s . 185s Exiting Picopore. 185s Processing in-progress files. Press Ctrl-C again to abort. 185s Complete. 185s Original size: 1898226 185s Compressed size: 2677464 186s Performing real time deep lossless compression... 186s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 186s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 205s .ERROR: Unable to open file (truncated file: eof = 2002944, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 215s . 215s Exiting Picopore. 215s Processing in-progress files. Press Ctrl-C again to abort. 215s Complete. 215s Original size: 1345266 215s Compressed size: 2632942 216s Performing real time raw compression with FASTQ and summary... 216s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 216s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 235s .ERROR: Unable to open file (truncated file: eof = 716800, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 246s . 247s Exiting Picopore. 247s Processing in-progress files. Press Ctrl-C again to abort. 247s Complete. 247s Original size: 1066738 247s Compressed size: 2123124 247s Performing real time raw compression with summary and no FASTQ... 247s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 247s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 266s .ERROR: Unable to open file (truncated file: eof = 589824, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 276s . 276s Exiting Picopore. 276s Processing in-progress files. Press Ctrl-C again to abort. 276s Complete. 276s Original size: 1263346 276s Compressed size: 2107577 277s Performing real time raw compression with FASTQ and no summary... 277s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 277s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 297s .ERROR: Unable to open file (truncated file: eof = 1253376, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 307s . 307s Exiting Picopore. 307s Processing in-progress files. Press Ctrl-C again to abort. 307s Complete. 307s Original size: 1427186 307s Compressed size: 2120708 308s Performing real time raw compression with no summary and no FASTQ... 308s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 308s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 327s .ERROR: Unable to open file (truncated file: eof = 1376256, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 337s . 337s Exiting Picopore. 337s Processing in-progress files. Press Ctrl-C again to abort. 337s Complete. 337s Original size: 1787634 337s Compressed size: 1954403 338s Performing real time raw compression with manual keyword Analyses... 338s Monitoring /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime in real time. Press Ctrl+C to exit. 338s No files found under /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime 358s .ERROR: Unable to open file (truncated file: eof = 1523712, sblock->base_addr = 0, stored_eof = 2003942) on file /tmp/autopkgtest.9TJtjC/autopkgtest_tmp/realtime/metrichor_2d_original.fast5 368s . 368s Exiting Picopore. 368s Processing in-progress files. Press Ctrl-C again to abort. 368s Complete. 368s Original size: 1234674 368s Compressed size: 2102857 368s python3 -m picopore -y --print-every 1 --test --mode lossless sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode lossless sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --test --mode deep-lossless sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode deep-lossless sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --fastq --summary sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --summary --no-fastq sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --fastq --no-summary sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --no-fastq --no-summary sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --manual Analyses sample_data/albacore_1d_original.fast5 368s python3 -m picopore -y --print-every 1 --test --mode lossless sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode lossless sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --test --mode deep-lossless sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode deep-lossless sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --fastq --summary sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --summary --no-fastq sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --fastq --no-summary sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --no-fastq --no-summary sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --print-every 1 --prefix picopore.test --mode raw --manual Analyses sample_data/metrichor_2d_original.fast5 368s python3 -m picopore -y --realtime --print-every 1 --mode lossless realtime 368s python3 -m picopore -y --realtime --print-every 1 --mode deep-lossless realtime 368s python3 -m picopore -y --realtime --print-every 1 --fastq --summary --mode raw realtime 368s python3 -m picopore -y --realtime --print-every 1 --summary --no-fastq --mode raw realtime 368s python3 -m picopore -y --realtime --print-every 1 --fastq --no-summary --mode raw realtime 368s python3 -m picopore -y --realtime --print-every 1 --no-fastq --no-summary --mode raw realtime 368s python3 -m picopore -y --realtime --print-every 1 --manual Analyses --mode raw realtime 368s PASS 369s autopkgtest [09:57:18]: test run-unit-test: -----------------------] 369s autopkgtest [09:57:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 369s run-unit-test PASS 369s autopkgtest [09:57:18]: test autodep8-python3: preparing testbed 492s autopkgtest [09:59:21]: testbed dpkg architecture: arm64 492s autopkgtest [09:59:21]: testbed apt version: 2.9.8 492s autopkgtest [09:59:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 493s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 493s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 493s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 494s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 494s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 494s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 494s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 494s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 494s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 494s Fetched 1794 kB in 2s (1170 kB/s) 494s Reading package lists... 497s Reading package lists... 497s Building dependency tree... 497s Reading state information... 498s Calculating upgrade... 498s The following NEW packages will be installed: 498s python3.13-gdbm 498s The following packages will be upgraded: 498s libpython3-stdlib python3 python3-gdbm python3-minimal 499s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 499s Need to get 101 kB of archives. 499s After this operation, 141 kB of additional disk space will be used. 499s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 499s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 499s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 499s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 499s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 499s Fetched 101 kB in 0s (287 kB/s) 500s (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 ... 79924 files and directories currently installed.) 500s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 500s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 500s Setting up python3-minimal (3.12.7-1) ... 500s (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 ... 79924 files and directories currently installed.) 500s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 500s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 500s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 500s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 500s Selecting previously unselected package python3.13-gdbm. 500s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 500s Unpacking python3.13-gdbm (3.13.0-2) ... 500s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 500s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 500s Setting up python3.13-gdbm (3.13.0-2) ... 500s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 500s Setting up python3 (3.12.7-1) ... 500s Setting up python3-gdbm:arm64 (3.12.7-1) ... 500s Processing triggers for man-db (2.12.1-3) ... 501s Reading package lists... 502s Building dependency tree... 502s Reading state information... 502s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 503s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 503s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 503s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 503s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 504s Reading package lists... 504s Reading package lists... 504s Building dependency tree... 504s Reading state information... 505s Calculating upgrade... 505s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 505s Reading package lists... 505s Building dependency tree... 505s Reading state information... 506s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 514s Reading package lists... 515s Building dependency tree... 515s Reading state information... 515s Starting pkgProblemResolver with broken count: 0 515s Starting 2 pkgProblemResolver with broken count: 0 515s Done 516s The following additional packages will be installed: 516s hdf5-tools libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 516s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblzf1 516s libpython3.13-minimal libpython3.13-stdlib libsz2 python3-all python3-h5py 516s python3-h5py-serial python3-numpy python3-picopore python3-watchdog 516s python3.13 python3.13-minimal 516s Suggested packages: 516s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 516s python3.13-venv python3.13-doc binfmt-support 516s Recommended packages: 516s javascript-common 516s The following NEW packages will be installed: 516s autopkgtest-satdep hdf5-tools libaec0 libblas3 libgfortran5 libhdf5-103-1t64 516s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 516s liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2 python3-all 516s python3-h5py python3-h5py-serial python3-numpy python3-picopore 516s python3-watchdog python3.13 python3.13-minimal 516s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 516s Need to get 15.7 MB/15.7 MB of archives. 516s After this operation, 65.9 MB of additional disk space will be used. 516s Get:1 /tmp/autopkgtest.9TJtjC/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 516s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 517s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 517s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 517s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 517s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 518s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 hdf5-tools arm64 1.10.10+repack-4ubuntu3 [319 kB] 518s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 518s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 518s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 518s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 518s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 518s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 518s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 518s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 518s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 519s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 519s Get:18 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 519s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 519s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 519s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 519s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-watchdog all 5.0.0-1 [125 kB] 519s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-picopore all 1.2.0-3 [15.6 kB] 520s Fetched 15.7 MB in 3s (4707 kB/s) 520s Selecting previously unselected package libpython3.13-minimal:arm64. 520s (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 ... 79931 files and directories currently installed.) 520s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 520s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 520s Selecting previously unselected package python3.13-minimal. 520s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 520s Unpacking python3.13-minimal (3.13.0-2) ... 520s Selecting previously unselected package libaec0:arm64. 520s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 520s Unpacking libaec0:arm64 (1.1.3-1) ... 520s Selecting previously unselected package libsz2:arm64. 520s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 520s Unpacking libsz2:arm64 (1.1.3-1) ... 520s Selecting previously unselected package libhdf5-103-1t64:arm64. 520s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 520s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 520s Selecting previously unselected package hdf5-tools. 520s Preparing to unpack .../05-hdf5-tools_1.10.10+repack-4ubuntu3_arm64.deb ... 520s Unpacking hdf5-tools (1.10.10+repack-4ubuntu3) ... 520s Selecting previously unselected package libblas3:arm64. 520s Preparing to unpack .../06-libblas3_3.12.0-3build2_arm64.deb ... 520s Unpacking libblas3:arm64 (3.12.0-3build2) ... 520s Selecting previously unselected package libgfortran5:arm64. 520s Preparing to unpack .../07-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 520s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 520s Selecting previously unselected package libhdf5-hl-100t64:arm64. 520s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 520s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 520s Selecting previously unselected package libjs-jquery. 520s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 520s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 520s Selecting previously unselected package libjs-underscore. 520s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 520s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 520s Selecting previously unselected package libjs-sphinxdoc. 520s Preparing to unpack .../11-libjs-sphinxdoc_7.4.7-4_all.deb ... 520s Unpacking libjs-sphinxdoc (7.4.7-4) ... 520s Selecting previously unselected package liblapack3:arm64. 520s Preparing to unpack .../12-liblapack3_3.12.0-3build2_arm64.deb ... 520s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 520s Selecting previously unselected package liblzf1:arm64. 520s Preparing to unpack .../13-liblzf1_3.6-4_arm64.deb ... 520s Unpacking liblzf1:arm64 (3.6-4) ... 520s Selecting previously unselected package libpython3.13-stdlib:arm64. 520s Preparing to unpack .../14-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 520s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 521s Selecting previously unselected package python3.13. 521s Preparing to unpack .../15-python3.13_3.13.0-2_arm64.deb ... 521s Unpacking python3.13 (3.13.0-2) ... 521s Selecting previously unselected package python3-all. 521s Preparing to unpack .../16-python3-all_3.12.7-1_arm64.deb ... 521s Unpacking python3-all (3.12.7-1) ... 521s Selecting previously unselected package python3-numpy. 521s Preparing to unpack .../17-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 521s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 521s Selecting previously unselected package python3-h5py-serial. 521s Preparing to unpack .../18-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 521s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 521s Selecting previously unselected package python3-h5py. 521s Preparing to unpack .../19-python3-h5py_3.11.0-5ubuntu1_all.deb ... 521s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 521s Selecting previously unselected package python3-watchdog. 521s Preparing to unpack .../20-python3-watchdog_5.0.0-1_all.deb ... 521s Unpacking python3-watchdog (5.0.0-1) ... 521s Selecting previously unselected package python3-picopore. 521s Preparing to unpack .../21-python3-picopore_1.2.0-3_all.deb ... 521s Unpacking python3-picopore (1.2.0-3) ... 521s Selecting previously unselected package autopkgtest-satdep. 521s Preparing to unpack .../22-2-autopkgtest-satdep.deb ... 521s Unpacking autopkgtest-satdep (0) ... 521s Setting up libaec0:arm64 (1.1.3-1) ... 521s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 521s Setting up libblas3:arm64 (3.12.0-3build2) ... 521s 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 521s Setting up liblzf1:arm64 (3.6-4) ... 521s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 521s Setting up python3.13-minimal (3.13.0-2) ... 522s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 522s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 522s Setting up libsz2:arm64 (1.1.3-1) ... 522s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 522s Setting up liblapack3:arm64 (3.12.0-3build2) ... 522s 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 522s Setting up python3.13 (3.13.0-2) ... 523s Setting up python3-all (3.12.7-1) ... 523s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 527s Setting up libjs-sphinxdoc (7.4.7-4) ... 527s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 527s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 527s Setting up python3-watchdog (5.0.0-1) ... 528s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 528s Setting up hdf5-tools (1.10.10+repack-4ubuntu3) ... 528s Setting up python3-h5py (3.11.0-5ubuntu1) ... 528s Setting up python3-picopore (1.2.0-3) ... 529s Setting up autopkgtest-satdep (0) ... 529s Processing triggers for systemd (256.5-2ubuntu4) ... 529s Processing triggers for man-db (2.12.1-3) ... 529s Processing triggers for libc-bin (2.40-1ubuntu3) ... 533s (Reading database ... 81914 files and directories currently installed.) 533s Removing autopkgtest-satdep (0) ... 535s autopkgtest [10:00:04]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import picopore; print(picopore)" ; done 535s autopkgtest [10:00:04]: test autodep8-python3: [----------------------- 535s Testing with python3.13: 535s Traceback (most recent call last): 535s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 535s from . import multiarray 535s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 535s from . import overrides 535s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 535s from numpy.core._multiarray_umath import ( 535s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 535s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 535s 535s During handling of the above exception, another exception occurred: 535s 535s Traceback (most recent call last): 535s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 535s from numpy.__config__ import show as show_config 535s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 535s from numpy.core._multiarray_umath import ( 535s ...<3 lines>... 535s ) 535s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 535s raise ImportError(msg) 535s ImportError: 535s 535s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 535s 535s Importing the numpy C-extensions failed. This error can happen for 535s many reasons, often due to issues with your setup or how NumPy was 535s installed. 535s 535s We have compiled some common reasons and troubleshooting tips at: 535s 535s https://numpy.org/devdocs/user/troubleshooting-importerror.html 535s 535s Please note and check the following: 535s 535s * The Python version is: Python3.13 from "/usr/bin/python3.13" 535s * The NumPy version is: "1.26.4" 535s 535s and make sure that they are the versions you expect. 535s Please carefully study the documentation linked above for further help. 535s 535s Original error was: No module named 'numpy.core._multiarray_umath' 535s 535s 535s The above exception was the direct cause of the following exception: 535s 535s Traceback (most recent call last): 535s File "", line 1, in 535s import picopore; print(picopore) 535s ^^^^^^^^^^^^^^^ 535s File "/usr/lib/python3/dist-packages/picopore/__init__.py", line 2, in 535s from picopore.util import log 535s File "/usr/lib/python3/dist-packages/picopore/util.py", line 19, in 535s import numpy as np 535s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 535s raise ImportError(msg) from e 535s ImportError: Error importing numpy: you should not try to import numpy from 535s its source directory; please exit the numpy source tree, and relaunch 535s your python interpreter from there. 537s autopkgtest [10:00:05]: test autodep8-python3: -----------------------] 537s autodep8-python3 FAIL non-zero exit status 1 537s autopkgtest [10:00:06]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 538s autopkgtest [10:00:07]: @@@@@@@@@@@@@@@@@@@@ summary 538s run-unit-test PASS 538s autodep8-python3 FAIL non-zero exit status 1 551s nova [W] Skipping flock in bos03-arm64 551s Creating nova instance adt-plucky-arm64-picopore-20241113-095109-juju-7f2275-prod-proposed-migration-environment-15-ec114827-fa4b-4829-84b0-f43888ac5342 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 551s nova [W] Skipping flock in bos03-arm64 551s Creating nova instance adt-plucky-arm64-picopore-20241113-095109-juju-7f2275-prod-proposed-migration-environment-15-ec114827-fa4b-4829-84b0-f43888ac5342 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...