0s autopkgtest [10:34:14]: starting date and time: 2024-11-13 10:34:14+0000 0s autopkgtest [10:34:14]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:34:14]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.tslg4a27/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 python-iow --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-20@bos03-arm64-16.secgroup --name adt-plucky-arm64-python-iow-20241113-103413-juju-7f2275-prod-proposed-migration-environment-20-9ffb274f-fc57-4b2a-bf0c-b2f9958c51bb --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --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/ 108s autopkgtest [10:36:02]: testbed dpkg architecture: arm64 109s autopkgtest [10:36:02]: testbed apt version: 2.9.8 109s autopkgtest [10:36:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 110s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 110s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 110s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 110s Fetched 1794 kB in 1s (2051 kB/s) 110s Reading package lists... 113s Reading package lists... 114s Building dependency tree... 114s Reading state information... 114s Calculating upgrade... 115s The following NEW packages will be installed: 116s python3.13-gdbm 116s The following packages will be upgraded: 116s libpython3-stdlib python3 python3-gdbm python3-minimal 116s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 116s Need to get 101 kB of archives. 116s After this operation, 141 kB of additional disk space will be used. 116s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 116s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 116s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 116s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 116s Fetched 101 kB in 0s (290 kB/s) 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 116s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 116s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 116s Setting up python3-minimal (3.12.7-1) ... 116s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 79924 files and directories currently installed.) 116s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 116s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 116s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 116s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 116s Selecting previously unselected package python3.13-gdbm. 116s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 116s Unpacking python3.13-gdbm (3.13.0-2) ... 116s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 116s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 116s Setting up python3.13-gdbm (3.13.0-2) ... 116s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 116s Setting up python3 (3.12.7-1) ... 117s Setting up python3-gdbm:arm64 (3.12.7-1) ... 117s Processing triggers for man-db (2.12.1-3) ... 117s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 119s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 119s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 119s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 120s Reading package lists... 120s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 122s Reading package lists... 122s Building dependency tree... 122s Reading state information... 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [10:36:20]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 127s autopkgtest [10:36:21]: @@@@@@@@@@@@@@@@@@@@ apt-source python-iow 129s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (dsc) [2353 B] 129s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (tar) [160 kB] 129s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-iow 1.0.7-1 (diff) [4720 B] 129s gpgv: Signature made Sat Aug 31 10:16:19 2024 UTC 129s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 129s gpgv: issuer "emollier@debian.org" 129s gpgv: Can't check signature: No public key 129s dpkg-source: warning: cannot verify inline signature for ./python-iow_1.0.7-1.dsc: no acceptable signature found 129s autopkgtest [10:36:23]: testing package python-iow version 1.0.7-1 129s autopkgtest [10:36:23]: build not needed 130s autopkgtest [10:36:24]: test run-unit-test: preparing testbed 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s Starting pkgProblemResolver with broken count: 0 135s Starting 2 pkgProblemResolver with broken count: 0 135s Done 135s The following additional packages will be installed: 135s libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 libhdf5-hl-100t64 135s liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib 135s libssw0 libsz2 python3-all python3-biom-format python3-click 135s python3-colorama python3-dateutil python3-decorator python3-h5py 135s python3-h5py-serial python3-hdmedians python3-iow python3-natsort 135s python3-numpy python3-packaging python3-pandas python3-pandas-lib 135s python3-patsy python3-scipy python3-six python3-skbio python3-statsmodels 135s python3-statsmodels-lib python3-tz python3.13 python3.13-minimal 135s Suggested packages: 135s python-biom-format-doc python-h5py-doc python-natsort-doc gcc gfortran 135s python-numpy-doc python3-dev python3-pytest python-pandas-doc 135s python-patsy-doc python-scipy-doc python-skbio-doc python-statsmodels-doc 135s python3.13-venv python3.13-doc binfmt-support 135s Recommended packages: 135s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 135s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 135s g++ | c++-compiler python3-pil python3-joblib python3-cvxopt 135s The following NEW packages will be installed: 135s autopkgtest-satdep libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 135s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal 135s libpython3.13-stdlib libssw0 libsz2 python3-all python3-biom-format 135s python3-click python3-colorama python3-dateutil python3-decorator 135s python3-h5py python3-h5py-serial python3-hdmedians python3-iow 135s python3-natsort python3-numpy python3-packaging python3-pandas 135s python3-pandas-lib python3-patsy python3-scipy python3-six python3-skbio 135s python3-statsmodels python3-statsmodels-lib python3-tz python3.13 135s python3.13-minimal 136s 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. 136s Need to get 47.9 MB/47.9 MB of archives. 136s After this operation, 219 MB of additional disk space will be used. 136s Get:1 /tmp/autopkgtest.2JCBzw/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 136s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 136s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 136s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 136s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 136s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 136s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 136s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 136s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 136s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 136s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 136s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 136s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 136s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 136s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 libssw0 arm64 1.1-15 [21.8 kB] 136s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 137s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 137s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 137s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB] 137s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B] 137s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 137s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 137s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB] 137s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 137s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 137s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB] 137s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB] 137s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 137s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 137s Get:30 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1 [137 kB] 137s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-hdmedians arm64 0.14.2-5.1build1 [116 kB] 137s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 137s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 137s Get:34 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-patsy all 0.5.6-1 [181 kB] 137s Get:35 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels-lib arm64 0.14.4+dfsg-1 [1627 kB] 137s Get:36 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-statsmodels all 0.14.4+dfsg-1 [5010 kB] 138s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-skbio arm64 0.6.2-3 [1391 kB] 138s Get:38 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iow arm64 1.0.7-1 [388 kB] 138s Fetched 47.9 MB in 2s (22.8 MB/s) 138s Selecting previously unselected package libpython3.13-minimal:arm64. 138s (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.) 138s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 138s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 138s Selecting previously unselected package python3.13-minimal. 138s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 138s Unpacking python3.13-minimal (3.13.0-2) ... 138s Selecting previously unselected package libaec0:arm64. 138s Preparing to unpack .../02-libaec0_1.1.3-1_arm64.deb ... 138s Unpacking libaec0:arm64 (1.1.3-1) ... 138s Selecting previously unselected package libblas3:arm64. 138s Preparing to unpack .../03-libblas3_3.12.0-3build2_arm64.deb ... 138s Unpacking libblas3:arm64 (3.12.0-3build2) ... 138s Selecting previously unselected package libgfortran5:arm64. 138s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 138s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 138s Selecting previously unselected package libgomp1:arm64. 138s Preparing to unpack .../05-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 138s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 138s Selecting previously unselected package libsz2:arm64. 138s Preparing to unpack .../06-libsz2_1.1.3-1_arm64.deb ... 138s Unpacking libsz2:arm64 (1.1.3-1) ... 138s Selecting previously unselected package libhdf5-103-1t64:arm64. 139s Preparing to unpack .../07-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 139s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 139s Selecting previously unselected package libhdf5-hl-100t64:arm64. 139s Preparing to unpack .../08-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 139s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 139s Selecting previously unselected package liblapack3:arm64. 139s Preparing to unpack .../09-liblapack3_3.12.0-3build2_arm64.deb ... 139s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 139s Selecting previously unselected package liblbfgsb0:arm64. 139s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 139s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 139s Selecting previously unselected package liblzf1:arm64. 139s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 139s Unpacking liblzf1:arm64 (3.6-4) ... 139s Selecting previously unselected package libpython3.13-stdlib:arm64. 139s Preparing to unpack .../12-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 139s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 139s Selecting previously unselected package libssw0:arm64. 139s Preparing to unpack .../13-libssw0_1.1-15_arm64.deb ... 139s Unpacking libssw0:arm64 (1.1-15) ... 139s Selecting previously unselected package python3.13. 139s Preparing to unpack .../14-python3.13_3.13.0-2_arm64.deb ... 139s Unpacking python3.13 (3.13.0-2) ... 139s Selecting previously unselected package python3-all. 139s Preparing to unpack .../15-python3-all_3.12.7-1_arm64.deb ... 139s Unpacking python3-all (3.12.7-1) ... 139s Selecting previously unselected package python3-numpy. 139s Preparing to unpack .../16-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 139s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 139s Selecting previously unselected package python3-h5py-serial. 139s Preparing to unpack .../17-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ... 139s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 139s Selecting previously unselected package python3-h5py. 139s Preparing to unpack .../18-python3-h5py_3.11.0-5ubuntu1_all.deb ... 139s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 139s Selecting previously unselected package python3-colorama. 139s Preparing to unpack .../19-python3-colorama_0.4.6-4_all.deb ... 139s Unpacking python3-colorama (0.4.6-4) ... 139s Selecting previously unselected package python3-click. 139s Preparing to unpack .../20-python3-click_8.1.7-2_all.deb ... 139s Unpacking python3-click (8.1.7-2) ... 139s Selecting previously unselected package python3-six. 140s Preparing to unpack .../21-python3-six_1.16.0-7_all.deb ... 140s Unpacking python3-six (1.16.0-7) ... 140s Selecting previously unselected package python3-dateutil. 140s Preparing to unpack .../22-python3-dateutil_2.9.0-2_all.deb ... 140s Unpacking python3-dateutil (2.9.0-2) ... 140s Selecting previously unselected package python3-tz. 140s Preparing to unpack .../23-python3-tz_2024.1-2_all.deb ... 140s Unpacking python3-tz (2024.1-2) ... 140s Selecting previously unselected package python3-pandas-lib:arm64. 140s Preparing to unpack .../24-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ... 140s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 140s Selecting previously unselected package python3-pandas. 140s Preparing to unpack .../25-python3-pandas_2.2.3+dfsg-5_all.deb ... 140s Unpacking python3-pandas (2.2.3+dfsg-5) ... 140s Selecting previously unselected package python3-decorator. 140s Preparing to unpack .../26-python3-decorator_5.1.1-5_all.deb ... 140s Unpacking python3-decorator (5.1.1-5) ... 140s Selecting previously unselected package python3-scipy. 140s Preparing to unpack .../27-python3-scipy_1.13.1-5_arm64.deb ... 140s Unpacking python3-scipy (1.13.1-5) ... 141s Selecting previously unselected package python3-biom-format. 141s Preparing to unpack .../28-python3-biom-format_2.1.16-1_arm64.deb ... 141s Unpacking python3-biom-format (2.1.16-1) ... 141s Selecting previously unselected package python3-hdmedians. 141s Preparing to unpack .../29-python3-hdmedians_0.14.2-5.1build1_arm64.deb ... 141s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 141s Selecting previously unselected package python3-natsort. 141s Preparing to unpack .../30-python3-natsort_8.0.2-2_all.deb ... 141s Unpacking python3-natsort (8.0.2-2) ... 141s Selecting previously unselected package python3-packaging. 141s Preparing to unpack .../31-python3-packaging_24.1-1_all.deb ... 141s Unpacking python3-packaging (24.1-1) ... 141s Selecting previously unselected package python3-patsy. 141s Preparing to unpack .../32-python3-patsy_0.5.6-1_all.deb ... 141s Unpacking python3-patsy (0.5.6-1) ... 141s Selecting previously unselected package python3-statsmodels-lib:arm64. 141s Preparing to unpack .../33-python3-statsmodels-lib_0.14.4+dfsg-1_arm64.deb ... 141s Unpacking python3-statsmodels-lib:arm64 (0.14.4+dfsg-1) ... 141s Selecting previously unselected package python3-statsmodels. 141s Preparing to unpack .../34-python3-statsmodels_0.14.4+dfsg-1_all.deb ... 141s Unpacking python3-statsmodels (0.14.4+dfsg-1) ... 141s Selecting previously unselected package python3-skbio. 141s Preparing to unpack .../35-python3-skbio_0.6.2-3_arm64.deb ... 141s Unpacking python3-skbio (0.6.2-3) ... 141s Selecting previously unselected package python3-iow. 141s Preparing to unpack .../36-python3-iow_1.0.7-1_arm64.deb ... 141s Unpacking python3-iow (1.0.7-1) ... 141s Selecting previously unselected package autopkgtest-satdep. 141s Preparing to unpack .../37-1-autopkgtest-satdep.deb ... 141s Unpacking autopkgtest-satdep (0) ... 141s Setting up python3-colorama (0.4.6-4) ... 142s Setting up libgomp1:arm64 (14.2.0-8ubuntu1) ... 142s Setting up python3-click (8.1.7-2) ... 142s Setting up libaec0:arm64 (1.1.3-1) ... 142s Setting up python3-tz (2024.1-2) ... 142s Setting up python3-natsort (8.0.2-2) ... 142s Setting up python3-six (1.16.0-7) ... 143s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 143s Setting up python3-decorator (5.1.1-5) ... 143s Setting up libblas3:arm64 (3.12.0-3build2) ... 143s 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 143s Setting up python3-packaging (24.1-1) ... 143s Setting up liblzf1:arm64 (3.6-4) ... 143s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 143s Setting up python3.13-minimal (3.13.0-2) ... 144s Setting up python3-dateutil (2.9.0-2) ... 144s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 144s Setting up libssw0:arm64 (1.1-15) ... 144s Setting up libsz2:arm64 (1.1.3-1) ... 144s Setting up liblapack3:arm64 (3.12.0-3build2) ... 144s 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 144s Setting up python3.13 (3.13.0-2) ... 146s Setting up python3-all (3.12.7-1) ... 146s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 150s Setting up python3-hdmedians (0.14.2-5.1build1) ... 150s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 150s Setting up python3-statsmodels-lib:arm64 (0.14.4+dfsg-1) ... 150s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 150s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 150s Setting up python3-scipy (1.13.1-5) ... 158s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ... 158s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 158s Setting up python3-patsy (0.5.6-1) ... 159s Setting up python3-pandas (2.2.3+dfsg-5) ... 170s Setting up python3-h5py (3.11.0-5ubuntu1) ... 171s Setting up python3-statsmodels (0.14.4+dfsg-1) ... 177s Setting up python3-biom-format (2.1.16-1) ... 177s Setting up python3-skbio (0.6.2-3) ... 179s Setting up python3-iow (1.0.7-1) ... 179s Setting up autopkgtest-satdep (0) ... 179s Processing triggers for systemd (256.5-2ubuntu4) ... 179s Processing triggers for man-db (2.12.1-3) ... 179s Processing triggers for libc-bin (2.40-1ubuntu3) ... 186s (Reading database ... 87581 files and directories currently installed.) 186s Removing autopkgtest-satdep (0) ... 188s autopkgtest [10:37:22]: test run-unit-test: [----------------------- 189s EEEE 189s ====================================================================== 189s ERROR: tests.test_bp (unittest.loader._FailedTest.tests.test_bp) 189s ---------------------------------------------------------------------- 189s ImportError: Failed to import test module: tests.test_bp 189s Traceback (most recent call last): 189s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 189s from . import multiarray 189s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 189s from . import overrides 189s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 189s from numpy.core._multiarray_umath import ( 189s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 189s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 189s 189s During handling of the above exception, another exception occurred: 189s 189s Traceback (most recent call last): 189s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 189s from numpy.__config__ import show as show_config 189s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 189s from numpy.core._multiarray_umath import ( 189s ...<3 lines>... 189s ) 189s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 189s raise ImportError(msg) 189s ImportError: 189s 189s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 189s 189s Importing the numpy C-extensions failed. This error can happen for 189s many reasons, often due to issues with your setup or how NumPy was 189s installed. 189s 189s We have compiled some common reasons and troubleshooting tips at: 189s 189s https://numpy.org/devdocs/user/troubleshooting-importerror.html 189s 189s Please note and check the following: 189s 189s * The Python version is: Python3.13 from "/usr/bin/python3.13" 189s * The NumPy version is: "1.26.4" 189s 189s and make sure that they are the versions you expect. 189s Please carefully study the documentation linked above for further help. 189s 189s Original error was: No module named 'numpy.core._multiarray_umath' 189s 189s 189s The above exception was the direct cause of the following exception: 189s 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 189s module = self._get_module_from_name(name) 189s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 189s __import__(name) 189s ~~~~~~~~~~^^^^^^ 189s File "/tmp/autopkgtest.2JCBzw/autopkgtest_tmp/tests/tests/test_bp.py", line 14, in 189s import numpy as np 189s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 189s raise ImportError(msg) from e 189s ImportError: Error importing numpy: you should not try to import numpy from 189s its source directory; please exit the numpy source tree, and relaunch 189s your python interpreter from there. 189s 189s 189s ====================================================================== 189s ERROR: tests.test_conv (unittest.loader._FailedTest.tests.test_conv) 189s ---------------------------------------------------------------------- 189s ImportError: Failed to import test module: tests.test_conv 189s Traceback (most recent call last): 189s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 24, in 189s from . import _debian_h5py_serial as _h5py 189s File "/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py", line 25, in 189s from . import _errors 189s 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) 189s 189s During handling of the above exception, another exception occurred: 189s 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 189s module = self._get_module_from_name(name) 189s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 189s __import__(name) 189s ~~~~~~~~~~^^^^^^ 189s File "/tmp/autopkgtest.2JCBzw/autopkgtest_tmp/tests/tests/test_conv.py", line 4, in 189s import skbio 189s File "/usr/lib/python3/dist-packages/skbio/__init__.py", line 12, in 189s import skbio.io # noqa 189s ^^^^^^^^^^^^^^^ 189s File "/usr/lib/python3/dist-packages/skbio/io/__init__.py", line 251, in 189s from .registry import write, read, sniff, create_format, io_registry 189s File "/usr/lib/python3/dist-packages/skbio/io/registry.py", line 181, in 189s from .util import _resolve_file, open_file, open_files, _d as _open_kwargs 189s File "/usr/lib/python3/dist-packages/skbio/io/util.py", line 32, in 189s from skbio.io._iosources import get_io_sources, get_compression_handler 189s File "/usr/lib/python3/dist-packages/skbio/io/_iosources.py", line 18, in 189s from ._fileobject import ( 189s ...<3 lines>... 189s ) 189s File "/usr/lib/python3/dist-packages/skbio/io/_fileobject.py", line 10, in 189s import h5py 189s File "/usr/lib/python3/dist-packages/h5py/__init__.py", line 26, in 189s from . import _debian_h5py_mpi as _h5py 189s 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) 189s 189s 189s ====================================================================== 189s ERROR: tests.test_insert (unittest.loader._FailedTest.tests.test_insert) 189s ---------------------------------------------------------------------- 189s ImportError: Failed to import test module: tests.test_insert 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 189s module = self._get_module_from_name(name) 189s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 189s __import__(name) 189s ~~~~~~~~~~^^^^^^ 189s File "/tmp/autopkgtest.2JCBzw/autopkgtest_tmp/tests/tests/test_insert.py", line 3, in 189s from bp import parse_jplace, insert_fully_resolved 189s File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in 189s from ._bp import BP 189s ModuleNotFoundError: No module named 'bp._bp' 189s 189s 189s ====================================================================== 189s ERROR: tests.test_io (unittest.loader._FailedTest.tests.test_io) 189s ---------------------------------------------------------------------- 189s ImportError: Failed to import test module: tests.test_io 189s Traceback (most recent call last): 189s File "/usr/lib/python3.13/unittest/loader.py", line 396, in _find_test_path 189s module = self._get_module_from_name(name) 189s File "/usr/lib/python3.13/unittest/loader.py", line 339, in _get_module_from_name 189s __import__(name) 189s ~~~~~~~~~~^^^^^^ 189s File "/tmp/autopkgtest.2JCBzw/autopkgtest_tmp/tests/tests/test_io.py", line 2, in 189s from bp import parse_newick, to_skbio_treenode, write_newick, parse_jplace 189s File "/usr/lib/python3/dist-packages/bp/__init__.py", line 8, in 189s from ._bp import BP 189s ModuleNotFoundError: No module named 'bp._bp' 189s 189s 189s ---------------------------------------------------------------------- 189s Ran 4 tests in 0.000s 189s 189s FAILED (errors=4) 191s .........................................../usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'e' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'f' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'g' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name None does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'l' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'a' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'b' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'd' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s /usr/lib/python3/dist-packages/skbio/tree/_tree.py:3287: RepresentationWarning: `TreeNode.tip_tip_distances`: Node with name 'c' does not have an associated length, so a length of 0.0 will be used. 191s warn( 191s ... 191s ---------------------------------------------------------------------- 191s Ran 46 tests in 0.284s 191s 191s OK 191s autopkgtest [10:37:25]: test run-unit-test: -----------------------] 192s autopkgtest [10:37:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 192s run-unit-test PASS 193s autopkgtest [10:37:27]: @@@@@@@@@@@@@@@@@@@@ summary 193s run-unit-test PASS 215s nova [W] Skipping flock in bos03-arm64 215s Creating nova instance adt-plucky-arm64-python-iow-20241113-103413-juju-7f2275-prod-proposed-migration-environment-20-9ffb274f-fc57-4b2a-bf0c-b2f9958c51bb from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...