0s autopkgtest [09:07:26]: starting date and time: 2024-11-13 09:07:26+0000 0s autopkgtest [09:07:26]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:07:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.n9ufgb2x/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 ont-fast5-api --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-2@lcy02-18.secgroup --name adt-plucky-amd64-ont-fast5-api-20241113-090726-juju-7f2275-prod-proposed-migration-environment-2-d85d5a1d-00dc-43fa-85b4-12797fd8582c --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 73s autopkgtest [09:08:39]: testbed dpkg architecture: amd64 73s autopkgtest [09:08:39]: testbed apt version: 2.9.8 73s autopkgtest [09:08:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 73s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 73s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 73s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 73s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 73s Fetched 2173 kB in 0s (5370 kB/s) 74s Reading package lists... 75s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Calculating upgrade... 76s The following NEW packages will be installed: 76s python3.13-gdbm 76s The following packages will be upgraded: 76s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 76s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 76s Need to get 253 kB of archives. 76s After this operation, 147 kB of additional disk space will be used. 76s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 76s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 76s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 77s Fetched 253 kB in 0s (5507 kB/s) 77s (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 ... 75541 files and directories currently installed.) 77s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 77s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Setting up python3-minimal (3.12.7-1) ... 77s (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 ... 75541 files and directories currently installed.) 77s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 77s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 77s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 77s Selecting previously unselected package python3.13-gdbm. 78s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 78s Unpacking python3.13-gdbm (3.13.0-2) ... 78s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 78s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 78s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 78s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 78s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 78s Setting up python3.13-gdbm (3.13.0-2) ... 78s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 78s Setting up python3 (3.12.7-1) ... 78s Setting up python3-gdbm:amd64 (3.12.7-1) ... 78s Processing triggers for man-db (2.12.1-3) ... 79s Processing triggers for libc-bin (2.40-1ubuntu3) ... 79s Reading package lists... 79s Building dependency tree... 79s Reading state information... 79s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 80s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 81s Reading package lists... 81s Reading package lists... 81s Building dependency tree... 81s Reading state information... 82s Calculating upgrade... 82s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Reading package lists... 82s Building dependency tree... 82s Reading state information... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s autopkgtest [09:08:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 84s autopkgtest [09:08:50]: @@@@@@@@@@@@@@@@@@@@ apt-source ont-fast5-api 85s Get:1 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (dsc) [2236 B] 85s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (tar) [1384 kB] 85s Get:3 http://ftpmaster.internal/ubuntu plucky/universe ont-fast5-api 4.1.1+dfsg-4 (diff) [4572 B] 85s gpgv: Signature made Wed Aug 28 16:17:26 2024 UTC 85s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 85s gpgv: issuer "tchet@debian.org" 85s gpgv: Can't check signature: No public key 85s dpkg-source: warning: cannot verify inline signature for ./ont-fast5-api_4.1.1+dfsg-4.dsc: no acceptable signature found 85s autopkgtest [09:08:51]: testing package ont-fast5-api version 4.1.1+dfsg-4 85s autopkgtest [09:08:51]: build not needed 85s autopkgtest [09:08:51]: test run-unit-test: preparing testbed 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 87s The following additional packages will be installed: 87s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 87s liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2 87s libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 ont-fast5-api python3-all 87s python3-h5py python3-h5py-serial python3-numpy python3-packaging 87s python3-progressbar python3.13 python3.13-minimal 87s Suggested packages: 87s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 87s python3.13-venv python3.13-doc binfmt-support 87s The following NEW packages will be installed: 87s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 87s libhdf5-hl-100t64 liblapack3 liblzf1 libpython3.13-minimal 87s libpython3.13-stdlib libsz2 libvbz-hdf-plugin-dev libvbz-hdf-plugin0t64 87s ont-fast5-api python3-all python3-h5py python3-h5py-serial python3-numpy 87s python3-packaging python3-progressbar python3.13 python3.13-minimal 87s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 87s Need to get 16.8 MB/16.8 MB of archives. 87s After this operation, 68.1 MB of additional disk space will be used. 87s Get:1 /tmp/autopkgtest.OQGhTJ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [724 B] 87s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 87s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 87s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 87s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 87s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 87s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 87s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 87s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 87s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 87s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 87s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 87s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 libvbz-hdf-plugin0t64 amd64 1.0.2-3.1build1 [20.3 kB] 87s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 libvbz-hdf-plugin-dev amd64 1.0.2-3.1build1 [14.4 kB] 87s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 87s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB] 87s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 87s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 87s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-progressbar all 2.5-4 [11.0 kB] 87s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 ont-fast5-api amd64 4.1.1+dfsg-4 [49.6 kB] 87s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 87s Get:22 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 88s Fetched 16.8 MB in 0s (41.0 MB/s) 88s Selecting previously unselected package libpython3.13-minimal:amd64. 88s (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 ... 75548 files and directories currently installed.) 88s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 88s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 88s Selecting previously unselected package python3.13-minimal. 88s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 88s Unpacking python3.13-minimal (3.13.0-2) ... 88s Selecting previously unselected package libaec0:amd64. 88s Preparing to unpack .../02-libaec0_1.1.3-1_amd64.deb ... 88s Unpacking libaec0:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libblas3:amd64. 88s Preparing to unpack .../03-libblas3_3.12.0-3build2_amd64.deb ... 88s Unpacking libblas3:amd64 (3.12.0-3build2) ... 88s Selecting previously unselected package libgfortran5:amd64. 88s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 88s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 88s Selecting previously unselected package libsz2:amd64. 88s Preparing to unpack .../05-libsz2_1.1.3-1_amd64.deb ... 88s Unpacking libsz2:amd64 (1.1.3-1) ... 88s Selecting previously unselected package libhdf5-103-1t64:amd64. 88s Preparing to unpack .../06-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 88s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 88s Selecting previously unselected package libhdf5-hl-100t64:amd64. 88s Preparing to unpack .../07-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 88s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 88s Selecting previously unselected package liblapack3:amd64. 88s Preparing to unpack .../08-liblapack3_3.12.0-3build2_amd64.deb ... 88s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 88s Selecting previously unselected package liblzf1:amd64. 88s Preparing to unpack .../09-liblzf1_3.6-4_amd64.deb ... 88s Unpacking liblzf1:amd64 (3.6-4) ... 88s Selecting previously unselected package libpython3.13-stdlib:amd64. 88s Preparing to unpack .../10-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 88s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 88s Selecting previously unselected package libvbz-hdf-plugin0t64:amd64. 88s Preparing to unpack .../11-libvbz-hdf-plugin0t64_1.0.2-3.1build1_amd64.deb ... 88s Unpacking libvbz-hdf-plugin0t64:amd64 (1.0.2-3.1build1) ... 88s Selecting previously unselected package libvbz-hdf-plugin-dev:amd64. 88s Preparing to unpack .../12-libvbz-hdf-plugin-dev_1.0.2-3.1build1_amd64.deb ... 88s Unpacking libvbz-hdf-plugin-dev:amd64 (1.0.2-3.1build1) ... 88s Selecting previously unselected package python3-numpy. 88s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 88s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 89s Selecting previously unselected package python3-h5py-serial. 89s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ... 89s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 89s Selecting previously unselected package python3-h5py. 89s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ... 89s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 89s Selecting previously unselected package python3-packaging. 89s Preparing to unpack .../16-python3-packaging_24.1-1_all.deb ... 89s Unpacking python3-packaging (24.1-1) ... 89s Selecting previously unselected package python3-progressbar. 89s Preparing to unpack .../17-python3-progressbar_2.5-4_all.deb ... 89s Unpacking python3-progressbar (2.5-4) ... 89s Selecting previously unselected package ont-fast5-api. 89s Preparing to unpack .../18-ont-fast5-api_4.1.1+dfsg-4_amd64.deb ... 89s Unpacking ont-fast5-api (4.1.1+dfsg-4) ... 89s Selecting previously unselected package python3.13. 89s Preparing to unpack .../19-python3.13_3.13.0-2_amd64.deb ... 89s Unpacking python3.13 (3.13.0-2) ... 89s Selecting previously unselected package python3-all. 89s Preparing to unpack .../20-python3-all_3.12.7-1_amd64.deb ... 89s Unpacking python3-all (3.12.7-1) ... 89s Selecting previously unselected package autopkgtest-satdep. 89s Preparing to unpack .../21-1-autopkgtest-satdep.deb ... 89s Unpacking autopkgtest-satdep (0) ... 89s Setting up libaec0:amd64 (1.1.3-1) ... 89s Setting up libvbz-hdf-plugin0t64:amd64 (1.0.2-3.1build1) ... 89s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 89s Setting up python3-progressbar (2.5-4) ... 89s Setting up libblas3:amd64 (3.12.0-3build2) ... 89s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 89s Setting up python3-packaging (24.1-1) ... 89s Setting up liblzf1:amd64 (3.6-4) ... 89s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 89s Setting up python3.13-minimal (3.13.0-2) ... 90s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 90s Setting up libsz2:amd64 (1.1.3-1) ... 90s Setting up liblapack3:amd64 (3.12.0-3build2) ... 90s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 90s Setting up libvbz-hdf-plugin-dev:amd64 (1.0.2-3.1build1) ... 90s Setting up python3.13 (3.13.0-2) ... 91s Setting up python3-all (3.12.7-1) ... 91s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 95s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 95s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 95s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 96s Setting up python3-h5py (3.11.0-5ubuntu1) ... 96s Setting up ont-fast5-api (4.1.1+dfsg-4) ... 96s Setting up autopkgtest-satdep (0) ... 96s Processing triggers for systemd (256.5-2ubuntu4) ... 96s Processing triggers for man-db (2.12.1-3) ... 96s Processing triggers for libc-bin (2.40-1ubuntu3) ... 99s (Reading database ... 77430 files and directories currently installed.) 99s Removing autopkgtest-satdep (0) ... 99s autopkgtest [09:09:05]: test run-unit-test: [----------------------- 100s test.test_alignment_tools (unittest.loader._FailedTest.test.test_alignment_tools) ... ERROR 100s test.test_basecall_1d_tools (unittest.loader._FailedTest.test.test_basecall_1d_tools) ... ERROR 100s test.test_basecall_2d_tools (unittest.loader._FailedTest.test.test_basecall_2d_tools) ... ERROR 100s test.test_check_compression (unittest.loader._FailedTest.test.test_check_compression) ... ERROR 100s test.test_compress_fast5 (unittest.loader._FailedTest.test.test_compress_fast5) ... ERROR 100s test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) ... ERROR 100s test.test_data_sanitisation (unittest.loader._FailedTest.test.test_data_sanitisation) ... ERROR 100s test.test_demux_fast5 (unittest.loader._FailedTest.test.test_demux_fast5) ... ERROR 100s test.test_event_detection_tools (unittest.loader._FailedTest.test.test_event_detection_tools) ... ERROR 100s test.test_fast5_conversion_utils (unittest.loader._FailedTest.test.test_fast5_conversion_utils) ... ERROR 100s test.test_fast5_converter (unittest.loader._FailedTest.test.test_fast5_converter) ... ERROR 100s test.test_fast5_file (unittest.loader._FailedTest.test.test_fast5_file) ... ERROR 100s test.test_fast5_interface (unittest.loader._FailedTest.test.test_fast5_interface) ... ERROR 100s test.test_fast5_subset (unittest.loader._FailedTest.test.test_fast5_subset) ... ERROR 100s test.test_hardlink_metadata (unittest.loader._FailedTest.test.test_hardlink_metadata) ... ERROR 100s test.test_multi_fast5 (unittest.loader._FailedTest.test.test_multi_fast5) ... ERROR 100s test.test_segmentation_tools (unittest.loader._FailedTest.test.test_segmentation_tools) ... ERROR 100s 100s ====================================================================== 100s ERROR: test.test_alignment_tools (unittest.loader._FailedTest.test.test_alignment_tools) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_alignment_tools 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_alignment_tools.py", line 2, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_basecall_1d_tools (unittest.loader._FailedTest.test.test_basecall_1d_tools) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_basecall_1d_tools 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_basecall_1d_tools.py", line 1, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_basecall_2d_tools (unittest.loader._FailedTest.test.test_basecall_2d_tools) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_basecall_2d_tools 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_basecall_2d_tools.py", line 1, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_check_compression (unittest.loader._FailedTest.test.test_check_compression) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_check_compression 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_check_compression.py", line 4, in 100s import numpy 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_compress_fast5 (unittest.loader._FailedTest.test.test_compress_fast5) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_compress_fast5 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_compress_fast5.py", line 1, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test_register_plugin_no_prepend (test.test_compression_settings.TestCheckCompression.test_register_plugin_no_prepend) 100s ---------------------------------------------------------------------- 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_compression_settings.py", line 11, in test_register_plugin_no_prepend 100s with patch('h5py.h5pl', create=True) as mock: 100s ~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^ 100s File "/usr/lib/python3.13/unittest/mock.py", line 1475, in __enter__ 100s self.target = self.getter() 100s ~~~~~~~~~~~^^ 100s File "/usr/lib/python3.13/pkgutil.py", line 513, in resolve_name 100s mod = importlib.import_module(modname) 100s File "/usr/lib/python3.13/importlib/__init__.py", line 88, in import_module 100s return _bootstrap._gcd_import(name[level:], package, level) 100s ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 100s File "", line 1387, in _gcd_import 100s File "", line 1360, in _find_and_load 100s File "", line 1331, in _find_and_load_unlocked 100s File "", line 935, in _load_unlocked 100s File "", line 1022, in exec_module 100s File "", line 488, in _call_with_frames_removed 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s ====================================================================== 100s ERROR: test.test_data_sanitisation (unittest.loader._FailedTest.test.test_data_sanitisation) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_data_sanitisation 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_data_sanitisation.py", line 1, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_demux_fast5 (unittest.loader._FailedTest.test.test_demux_fast5) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_demux_fast5 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_demux_fast5.py", line 4, in 100s from ont_fast5_api.conversion_tools.demux_fast5 import Fast5Demux 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/demux_fast5.py", line 16, in 100s from ont_fast5_api.conversion_tools.conversion_utils import ( 100s ...<6 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/conversion_utils.py", line 12, in 100s from ont_fast5_api.fast5_interface import get_fast5_file 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_interface.py", line 2, in 100s from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_event_detection_tools (unittest.loader._FailedTest.test.test_event_detection_tools) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_event_detection_tools 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_event_detection_tools.py", line 2, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_fast5_conversion_utils (unittest.loader._FailedTest.test.test_fast5_conversion_utils) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_fast5_conversion_utils 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_fast5_conversion_utils.py", line 2, in 100s from ont_fast5_api.fast5_read import Fast5Read 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_read.py", line 4, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_fast5_converter (unittest.loader._FailedTest.test.test_fast5_converter) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_fast5_converter 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_fast5_converter.py", line 5, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_fast5_file (unittest.loader._FailedTest.test.test_fast5_file) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_fast5_file 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_fast5_file.py", line 11, in 100s from ont_fast5_api.fast5_info import Fast5Info, _clean 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_info.py", line 4, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_fast5_interface (unittest.loader._FailedTest.test.test_fast5_interface) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_fast5_interface 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_fast5_interface.py", line 4, in 100s from ont_fast5_api.fast5_file import Fast5File 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_fast5_subset (unittest.loader._FailedTest.test.test_fast5_subset) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_fast5_subset 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_fast5_subset.py", line 2, in 100s import numpy 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_hardlink_metadata (unittest.loader._FailedTest.test.test_hardlink_metadata) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_hardlink_metadata 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 100s from . import _debian_h5py_serial as _h5py 100s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 100s from . import _errors 100s ImportError: cannot import name '_errors' from partially initialized module 'h5py._debian_h5py_serial' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py) 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_hardlink_metadata.py", line 4, in 100s from ont_fast5_api.conversion_tools.compress_fast5 import compress_file 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/compress_fast5.py", line 9, in 100s from ont_fast5_api.conversion_tools.conversion_utils import get_fast5_file_list, get_progress_bar 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/conversion_tools/conversion_utils.py", line 12, in 100s from ont_fast5_api.fast5_interface import get_fast5_file 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_interface.py", line 2, in 100s from ont_fast5_api.fast5_file import Fast5File, Fast5FileTypeError 100s File "/usr/lib/python3/dist-packages/ont_fast5_api/fast5_file.py", line 4, in 100s import h5py 100s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 100s from . import _debian_h5py_mpi as _h5py 100s ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py) 100s 100s 100s ====================================================================== 100s ERROR: test.test_multi_fast5 (unittest.loader._FailedTest.test.test_multi_fast5) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_multi_fast5 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_multi_fast5.py", line 1, in 100s import numpy 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ====================================================================== 100s ERROR: test.test_segmentation_tools (unittest.loader._FailedTest.test.test_segmentation_tools) 100s ---------------------------------------------------------------------- 100s ImportError: Failed to import test module: test.test_segmentation_tools 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 100s from . import multiarray 100s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 100s from . import overrides 100s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 100s from numpy.core._multiarray_umath import ( 100s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 100s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 100s 100s During handling of the above exception, another exception occurred: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 100s from numpy.__config__ import show as show_config 100s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 100s from numpy.core._multiarray_umath import ( 100s ...<3 lines>... 100s ) 100s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 100s raise ImportError(msg) 100s ImportError: 100s 100s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 100s 100s Importing the numpy C-extensions failed. This error can happen for 100s many reasons, often due to issues with your setup or how NumPy was 100s installed. 100s 100s We have compiled some common reasons and troubleshooting tips at: 100s 100s https://numpy.org/devdocs/user/troubleshooting-importerror.html 100s 100s Please note and check the following: 100s 100s * The Python version is: Python3.13 from "/usr/bin/python3.13" 100s * The NumPy version is: "1.26.4" 100s 100s and make sure that they are the versions you expect. 100s Please carefully study the documentation linked above for further help. 100s 100s Original error was: No module named 'numpy.core._multiarray_umath' 100s 100s 100s The above exception was the direct cause of the following exception: 100s 100s Traceback (most recent call last): 100s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 100s module = self._get_module_from_name(name) 100s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 100s __import__(name) 100s ~~~~~~~~~~^^^^^^ 100s File "/tmp/autopkgtest.OQGhTJ/autopkgtest_tmp/test/test_segmentation_tools.py", line 2, in 100s import numpy as np 100s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 100s raise ImportError(msg) from e 100s ImportError: Error importing numpy: you should not try to import numpy from 100s its source directory; please exit the numpy source tree, and relaunch 100s your python interpreter from there. 100s 100s 100s ---------------------------------------------------------------------- 100s Ran 17 tests in 0.005s 100s 100s FAILED (errors=17) 100s autopkgtest [09:09:06]: test run-unit-test: -----------------------] 101s run-unit-test FAIL non-zero exit status 1 101s autopkgtest [09:09:07]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 101s autopkgtest [09:09:07]: @@@@@@@@@@@@@@@@@@@@ summary 101s run-unit-test FAIL non-zero exit status 1 105s virt: nova [W] Skipping flock for amd64 105s virt: Creating nova instance adt-plucky-amd64-ont-fast5-api-20241113-090726-juju-7f2275-prod-proposed-migration-environment-2-d85d5a1d-00dc-43fa-85b4-12797fd8582c from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 76b850f9-98f4-4b79-af06-fa11000b95b2)...