0s autopkgtest [13:15:14]: starting date and time: 2025-02-19 13:15:14+0000 0s autopkgtest [13:15:14]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [13:15:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.jz7uc8yj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:sphinx --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-19.secgroup --name adt-plucky-amd64-python-biom-format-20250219-131514-juju-7f2275-prod-proposed-migration-environment-2-dc851108-dc3a-4b55-b63d-704a90221ce3 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 92s autopkgtest [13:16:46]: testbed dpkg architecture: amd64 92s autopkgtest [13:16:46]: testbed apt version: 2.9.29 92s autopkgtest [13:16:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 93s autopkgtest [13:16:47]: testbed release detected to be: None 93s autopkgtest [13:16:47]: updating testbed package index (apt update) 94s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 94s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 94s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 94s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 94s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 94s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 94s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 95s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 95s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [92.7 kB] 95s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 95s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 95s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 95s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [711 kB] 95s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [262 kB] 95s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 95s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 95s Fetched 2150 kB in 1s (2233 kB/s) 96s Reading package lists... 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Calculating upgrade... 97s The following NEW packages will be installed: 97s libapt-pkg7.0 97s The following packages will be upgraded: 97s apt apt-utils iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof rsyslog 97s sysvinit-utils 97s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 5425 kB of archives. 97s After this operation, 4076 kB of additional disk space will be used. 97s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sysvinit-utils amd64 3.14-1ubuntu1 [35.7 kB] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 98s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 98s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 98s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 98s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 98s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 98s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 98s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 98s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu1 [155 kB] 98s Preconfiguring packages ... 98s Fetched 5425 kB in 1s (6628 kB/s) 98s (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 ... 108925 files and directories currently installed.) 98s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_amd64.deb ... 98s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 98s Setting up sysvinit-utils (3.14-1ubuntu1) ... 98s Selecting previously unselected package libapt-pkg7.0:amd64. 99s (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 ... 108925 files and directories currently installed.) 99s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 99s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 99s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 99s (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 ... 108974 files and directories currently installed.) 99s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 99s Unpacking apt (2.9.30) over (2.9.29) ... 99s Setting up apt (2.9.30) ... 100s (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 ... 108974 files and directories currently installed.) 100s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 100s Unpacking apt-utils (2.9.30) over (2.9.29) ... 100s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 100s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 100s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 100s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 100s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 100s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 100s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 100s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 100s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 100s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 100s Preparing to unpack .../6-libgpgme11t64_1.24.2-1ubuntu1_amd64.deb ... 100s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 100s Setting up apt-utils (2.9.30) ... 100s Setting up liblsof0 (4.99.4+dfsg-1) ... 100s Setting up iproute2 (6.13.0-1ubuntu1) ... 100s Setting up rsyslog (8.2412.0-2ubuntu1) ... 100s info: The user `syslog' is already a member of `adm'. 102s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 102s Setting up lsof (4.99.4+dfsg-1) ... 102s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu1) ... 102s Processing triggers for man-db (2.13.0-1) ... 103s Processing triggers for libc-bin (2.40-4ubuntu1) ... 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s autopkgtest [13:16:59]: upgrading testbed (apt dist-upgrade and autopurge) 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 106s Starting 2 pkgProblemResolver with broken count: 0 106s Done 106s Entering ResolveByKeep 107s 107s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 108s Starting pkgProblemResolver with broken count: 0 108s Starting 2 pkgProblemResolver with broken count: 0 108s Done 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s autopkgtest [13:17:03]: rebooting testbed after setup commands that affected boot 132s autopkgtest [13:17:26]: testbed running kernel: Linux 6.12.0-15-generic #15-Ubuntu SMP PREEMPT_DYNAMIC Tue Feb 4 16:02:16 UTC 2025 135s autopkgtest [13:17:29]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 139s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (dsc) [2498 B] 139s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (tar) [11.9 MB] 139s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (diff) [11.7 kB] 139s gpgv: Signature made Wed Jan 29 22:35:10 2025 UTC 139s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build2.dsc: no acceptable signature found 140s autopkgtest [13:17:34]: testing package python-biom-format version 2.1.16-1build2 140s autopkgtest [13:17:34]: build not needed 143s autopkgtest [13:17:37]: test run-unit-test: preparing testbed 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Starting pkgProblemResolver with broken count: 0 144s Starting 2 pkgProblemResolver with broken count: 0 144s Done 144s The following NEW packages will be installed: 144s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 libjs-jquery 144s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 144s python-biom-format-doc python3-biom-format python3-click python3-dateutil 144s python3-decorator python3-h5py python3-h5py-serial python3-numpy 144s python3-pandas python3-pandas-lib python3-pytz python3-scipy python3-tz 145s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 145s Need to get 47.8 MB of archives. 145s After this operation, 264 MB of additional disk space will be used. 145s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 145s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 145s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 145s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 145s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 145s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 145s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 145s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 145s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 145s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 145s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biom-format-doc all 2.1.16-1build2 [57.5 kB] 145s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 145s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.12.1-1 [1677 kB] 145s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.12.1-1 [7970 B] 145s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.8-1 [79.8 kB] 145s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 145s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 145s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 145s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 146s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 146s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 146s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 147s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1build2 [186 kB] 147s Fetched 47.8 MB in 2s (21.3 MB/s) 147s Selecting previously unselected package libaec0:amd64. 147s (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 ... 108975 files and directories currently installed.) 147s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 147s Unpacking libaec0:amd64 (1.1.3-1) ... 147s Selecting previously unselected package libblas3:amd64. 147s Preparing to unpack .../01-libblas3_3.12.1-2_amd64.deb ... 147s Unpacking libblas3:amd64 (3.12.1-2) ... 147s Selecting previously unselected package libgfortran5:amd64. 147s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 147s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 147s Selecting previously unselected package libsz2:amd64. 147s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ... 147s Unpacking libsz2:amd64 (1.1.3-1) ... 147s Selecting previously unselected package libhdf5-310:amd64. 147s Preparing to unpack .../04-libhdf5-310_1.14.5+repack-3_amd64.deb ... 147s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 147s Selecting previously unselected package libhdf5-hl-310:amd64. 147s Preparing to unpack .../05-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 147s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 148s Selecting previously unselected package libjs-jquery. 148s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 148s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 148s Selecting previously unselected package libjs-underscore. 148s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 148s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 148s Selecting previously unselected package libjs-sphinxdoc. 148s Preparing to unpack .../08-libjs-sphinxdoc_8.1.3-5_all.deb ... 148s Unpacking libjs-sphinxdoc (8.1.3-5) ... 148s Selecting previously unselected package liblapack3:amd64. 148s Preparing to unpack .../09-liblapack3_3.12.1-2_amd64.deb ... 148s Unpacking liblapack3:amd64 (3.12.1-2) ... 148s Selecting previously unselected package liblbfgsb0:amd64. 148s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 148s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 148s Selecting previously unselected package liblzf1:amd64. 148s Preparing to unpack .../11-liblzf1_3.6-4_amd64.deb ... 148s Unpacking liblzf1:amd64 (3.6-4) ... 148s Selecting previously unselected package python-biom-format-doc. 148s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build2_all.deb ... 148s Unpacking python-biom-format-doc (2.1.16-1build2) ... 148s Selecting previously unselected package python3-numpy. 148s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 148s Unpacking python3-numpy (1:1.26.4+ds-13) ... 148s Selecting previously unselected package python3-h5py-serial. 148s Preparing to unpack .../14-python3-h5py-serial_3.12.1-1_amd64.deb ... 148s Unpacking python3-h5py-serial (3.12.1-1) ... 148s Selecting previously unselected package python3-h5py. 148s Preparing to unpack .../15-python3-h5py_3.12.1-1_all.deb ... 148s Unpacking python3-h5py (3.12.1-1) ... 148s Selecting previously unselected package python3-click. 148s Preparing to unpack .../16-python3-click_8.1.8-1_all.deb ... 148s Unpacking python3-click (8.1.8-1) ... 148s Selecting previously unselected package python3-dateutil. 148s Preparing to unpack .../17-python3-dateutil_2.9.0-3_all.deb ... 148s Unpacking python3-dateutil (2.9.0-3) ... 148s Selecting previously unselected package python3-pytz. 148s Preparing to unpack .../18-python3-pytz_2025.1-3_all.deb ... 148s Unpacking python3-pytz (2025.1-3) ... 148s Selecting previously unselected package python3-tz. 148s Preparing to unpack .../19-python3-tz_2025.1-3_all.deb ... 148s Unpacking python3-tz (2025.1-3) ... 148s Selecting previously unselected package python3-pandas-lib:amd64. 148s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... 148s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 148s Selecting previously unselected package python3-pandas. 148s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-8_all.deb ... 148s Unpacking python3-pandas (2.2.3+dfsg-8) ... 149s Selecting previously unselected package python3-decorator. 149s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 149s Unpacking python3-decorator (5.1.1-5) ... 149s Selecting previously unselected package python3-scipy. 149s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 149s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 149s Selecting previously unselected package python3-biom-format. 149s Preparing to unpack .../24-python3-biom-format_2.1.16-1build2_amd64.deb ... 149s Unpacking python3-biom-format (2.1.16-1build2) ... 149s Setting up python3-pytz (2025.1-3) ... 150s Setting up python3-click (8.1.8-1) ... 150s Setting up libaec0:amd64 (1.1.3-1) ... 150s Setting up python3-tz (2025.1-3) ... 150s Setting up python3-decorator (5.1.1-5) ... 150s Setting up libblas3:amd64 (3.12.1-2) ... 150s 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 150s Setting up liblzf1:amd64 (3.6-4) ... 150s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 150s Setting up python3-dateutil (2.9.0-3) ... 150s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 150s Setting up libsz2:amd64 (1.1.3-1) ... 150s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 150s Setting up liblapack3:amd64 (3.12.1-2) ... 150s 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 150s Setting up python3-numpy (1:1.26.4+ds-13) ... 151s Setting up libjs-sphinxdoc (8.1.3-5) ... 151s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 151s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 151s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 151s Setting up python3-scipy (1.14.1-4ubuntu1) ... 154s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 154s Setting up python3-h5py-serial (3.12.1-1) ... 154s Setting up python-biom-format-doc (2.1.16-1build2) ... 154s Setting up python3-pandas (2.2.3+dfsg-8) ... 158s Setting up python3-h5py (3.12.1-1) ... 158s Setting up python3-biom-format (2.1.16-1build2) ... 158s Processing triggers for man-db (2.13.0-1) ... 159s Processing triggers for libc-bin (2.40-4ubuntu1) ... 160s autopkgtest [13:17:54]: test run-unit-test: [----------------------- 161s 161s System information 161s ================== 161s Platform: linux 161s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 161s Python executable: /usr/bin/python3 161s 161s Dependency versions 161s =================== 161s click version: 8.1.8 161s NumPy version: 1.26.4 161s SciPy version: 1.14.1 161s h5py version: 3.12.1 161s 161s biom-format package information 161s =============================== 161s biom-format version: 2.1.16 161s 162s 162s The input file is a valid BIOM-formatted file. 163s 163s The input file is a valid BIOM-formatted file. 163s 163s The input file is a valid BIOM-formatted file. 164s 164s The input file is a valid BIOM-formatted file. 165s + table=examples/min_sparse_otu_table_hdf5.biom 165s + obsmd=examples/obs_md.txt 165s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 165s + biom show-install-info 166s 166s System information 166s ================== 166s Platform: linux 166s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 166s Python executable: /usr/bin/python3 166s 166s Dependency versions 166s =================== 166s click version: 8.1.8 166s NumPy version: 1.26.4 166s SciPy version: 1.14.1 166s h5py version: 3.12.1 166s 166s biom-format package information 166s =============================== 166s biom-format version: 2.1.16 166s 166s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 166s 166s The input file is a valid BIOM-formatted file. 167s + biom add-metadata -i examples/min_sparse_otu_table_hdf5.biom -o test_add_metadata.biom --observation-metadata-fp examples/obs_md.txt --sc-separated taxonomy 167s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 168s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 169s + biom validate-table -i test_json.biom 169s 169s The input file is a valid BIOM-formatted file. 169s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 170s + biom validate-table -i test_hdf5.biom 170s 170s The input file is a valid BIOM-formatted file. 171s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 171s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 172s + biom validate-table -i test_hdf5.biom 173s 173s The input file is a valid BIOM-formatted file. 173s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 173s + biom validate-table -i test_json.biom 174s 174s The input file is a valid BIOM-formatted file. 174s + biom head -i examples/min_sparse_otu_table_hdf5.biom 175s # Constructed from biom file 175s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 175s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 175s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 175s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 175s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 175s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 175s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 175s Sample1 175s Sample2 175s Sample3 175s Sample4 175s Sample5 175s Sample6 175s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 176s + cat 176s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 177s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 177s Num samples: 6 177s Num observations: 5 177s Total count: 27 177s Table density (fraction of non-zero values): 0.500 177s 177s Counts/sample summary: 177s Min: 3.000 177s Max: 7.000 177s Median: 4.000 177s Mean: 4.500 177s Std. dev.: 1.500 177s Sample Metadata Categories: None provided 177s Observation Metadata Categories: None provided 177s 177s Counts/sample detail: 177s Sample2: 3.000 177s Sample5: 3.000 177s Sample3: 4.000 177s Sample6: 4.000 177s Sample4: 6.000 177s Sample1: 7.000 178s + cat 178s + biom from-uc -i uctest -o test_uc.biom 178s If this message was shown, then all commands executed without failure 178s + echo If this message was shown, then all commands executed without failure 179s autopkgtest [13:18:13]: test run-unit-test: -----------------------] 179s autopkgtest [13:18:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 179s run-unit-test PASS 179s autopkgtest [13:18:13]: test autodep8-python3: preparing testbed 293s autopkgtest [13:20:07]: testbed dpkg architecture: amd64 293s autopkgtest [13:20:07]: testbed apt version: 2.9.29 294s autopkgtest [13:20:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup 294s autopkgtest [13:20:08]: testbed release detected to be: plucky 295s autopkgtest [13:20:09]: updating testbed package index (apt update) 295s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 296s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 296s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 296s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 296s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [744 kB] 296s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 296s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 296s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 296s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [92.7 kB] 296s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 296s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [7984 B] 296s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2412 B] 296s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [711 kB] 296s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [262 kB] 296s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [3128 B] 296s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [11.5 kB] 296s Fetched 2150 kB in 1s (2282 kB/s) 297s Reading package lists... 298s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Calculating upgrade... 299s The following NEW packages will be installed: 299s libapt-pkg7.0 299s The following packages will be upgraded: 299s apt apt-utils iproute2 libgpgme11t64 liblsof0 libp11-kit0 lsof rsyslog 299s sysvinit-utils 299s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 299s Need to get 5425 kB of archives. 299s After this operation, 4076 kB of additional disk space will be used. 299s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 sysvinit-utils amd64 3.14-1ubuntu1 [35.7 kB] 299s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libapt-pkg7.0 amd64 2.9.30 [1131 kB] 300s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 apt amd64 2.9.30 [1434 kB] 300s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 apt-utils amd64 2.9.30 [222 kB] 300s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 iproute2 amd64 6.13.0-1ubuntu1 [1277 kB] 300s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libp11-kit0 amd64 0.25.5-2ubuntu3 [311 kB] 300s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 rsyslog amd64 8.2412.0-2ubuntu1 [555 kB] 300s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 lsof amd64 4.99.4+dfsg-1 [245 kB] 300s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsof0 amd64 4.99.4+dfsg-1 [59.6 kB] 300s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.24.2-1ubuntu1 [155 kB] 300s Preconfiguring packages ... 300s Fetched 5425 kB in 1s (6966 kB/s) 301s (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 ... 108925 files and directories currently installed.) 301s Preparing to unpack .../sysvinit-utils_3.14-1ubuntu1_amd64.deb ... 301s Unpacking sysvinit-utils (3.14-1ubuntu1) over (3.08-6ubuntu3) ... 301s Setting up sysvinit-utils (3.14-1ubuntu1) ... 301s Selecting previously unselected package libapt-pkg7.0:amd64. 301s (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 ... 108925 files and directories currently installed.) 301s Preparing to unpack .../libapt-pkg7.0_2.9.30_amd64.deb ... 301s Unpacking libapt-pkg7.0:amd64 (2.9.30) ... 301s Setting up libapt-pkg7.0:amd64 (2.9.30) ... 301s (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 ... 108974 files and directories currently installed.) 301s Preparing to unpack .../archives/apt_2.9.30_amd64.deb ... 301s Unpacking apt (2.9.30) over (2.9.29) ... 301s Setting up apt (2.9.30) ... 302s (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 ... 108974 files and directories currently installed.) 302s Preparing to unpack .../0-apt-utils_2.9.30_amd64.deb ... 302s Unpacking apt-utils (2.9.30) over (2.9.29) ... 302s Preparing to unpack .../1-iproute2_6.13.0-1ubuntu1_amd64.deb ... 302s Unpacking iproute2 (6.13.0-1ubuntu1) over (6.10.0-2ubuntu1) ... 302s Preparing to unpack .../2-libp11-kit0_0.25.5-2ubuntu3_amd64.deb ... 302s Unpacking libp11-kit0:amd64 (0.25.5-2ubuntu3) over (0.25.5-2ubuntu2) ... 303s Preparing to unpack .../3-rsyslog_8.2412.0-2ubuntu1_amd64.deb ... 303s Unpacking rsyslog (8.2412.0-2ubuntu1) over (8.2412.0-1ubuntu1) ... 303s Preparing to unpack .../4-lsof_4.99.4+dfsg-1_amd64.deb ... 303s Unpacking lsof (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 303s Preparing to unpack .../5-liblsof0_4.99.4+dfsg-1_amd64.deb ... 303s Unpacking liblsof0 (4.99.4+dfsg-1) over (4.99.3+dfsg-2) ... 303s Preparing to unpack .../6-libgpgme11t64_1.24.2-1ubuntu1_amd64.deb ... 303s Unpacking libgpgme11t64:amd64 (1.24.2-1ubuntu1) over (1.24.1-4ubuntu1) ... 303s Setting up apt-utils (2.9.30) ... 303s Setting up liblsof0 (4.99.4+dfsg-1) ... 303s Setting up iproute2 (6.13.0-1ubuntu1) ... 303s Setting up rsyslog (8.2412.0-2ubuntu1) ... 303s info: The user `syslog' is already a member of `adm'. 304s Setting up libp11-kit0:amd64 (0.25.5-2ubuntu3) ... 304s Setting up lsof (4.99.4+dfsg-1) ... 304s Setting up libgpgme11t64:amd64 (1.24.2-1ubuntu1) ... 304s Processing triggers for man-db (2.13.0-1) ... 306s Processing triggers for libc-bin (2.40-4ubuntu1) ... 308s Reading package lists... 308s Building dependency tree... 308s Reading state information... 308s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 308s autopkgtest [13:20:22]: upgrading testbed (apt dist-upgrade and autopurge) 309s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 309s Starting 2 pkgProblemResolver with broken count: 0 309s Done 310s Entering ResolveByKeep 310s 311s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 311s Reading package lists... 311s Building dependency tree... 311s Reading state information... 312s Starting pkgProblemResolver with broken count: 0 312s Starting 2 pkgProblemResolver with broken count: 0 312s Done 312s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 313s autopkgtest [13:20:27]: rebooting testbed after setup commands that affected boot 340s Reading package lists... 341s Building dependency tree... 341s Reading state information... 341s Starting pkgProblemResolver with broken count: 0 341s Starting 2 pkgProblemResolver with broken count: 0 341s Done 342s The following NEW packages will be installed: 342s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 342s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 342s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 342s python3-numpy python3-pandas python3-pandas-lib python3-pytz python3-scipy 342s python3-tz python3.12 python3.12-minimal 342s 0 upgraded, 24 newly installed, 0 to remove and 0 not upgraded. 342s Need to get 50.3 MB of archives. 342s After this operation, 272 MB of additional disk space will be used. 342s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12-minimal amd64 3.12.9-1 [2348 kB] 342s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.12 amd64 3.12.9-1 [671 kB] 342s Get:3 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 342s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.1-2 [359 kB] 342s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 15-20250213-1ubuntu1 [920 kB] 342s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 342s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-310 amd64 1.14.5+repack-3 [1519 kB] 342s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-310 amd64 1.14.5+repack-3 [62.6 kB] 342s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.1-2 [3179 kB] 343s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 343s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 343s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.13.1-1~exp2 [894 B] 343s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-13 [5319 kB] 343s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.12.1-1 [1677 kB] 343s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.12.1-1 [7970 B] 343s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.8-1 [79.8 kB] 343s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 343s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-pytz all 2025.1-3 [162 kB] 343s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2025.1-3 [1866 B] 343s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-8 [8248 kB] 343s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-8 [3112 kB] 343s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 343s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.14.1-4ubuntu1 [22.3 MB] 344s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1build2 [186 kB] 345s Fetched 50.3 MB in 3s (17.4 MB/s) 345s Selecting previously unselected package python3.12-minimal. 345s (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 ... 108975 files and directories currently installed.) 345s Preparing to unpack .../00-python3.12-minimal_3.12.9-1_amd64.deb ... 345s Unpacking python3.12-minimal (3.12.9-1) ... 345s Selecting previously unselected package python3.12. 345s Preparing to unpack .../01-python3.12_3.12.9-1_amd64.deb ... 345s Unpacking python3.12 (3.12.9-1) ... 345s Selecting previously unselected package libaec0:amd64. 345s Preparing to unpack .../02-libaec0_1.1.3-1_amd64.deb ... 345s Unpacking libaec0:amd64 (1.1.3-1) ... 345s Selecting previously unselected package libblas3:amd64. 345s Preparing to unpack .../03-libblas3_3.12.1-2_amd64.deb ... 345s Unpacking libblas3:amd64 (3.12.1-2) ... 345s Selecting previously unselected package libgfortran5:amd64. 345s Preparing to unpack .../04-libgfortran5_15-20250213-1ubuntu1_amd64.deb ... 345s Unpacking libgfortran5:amd64 (15-20250213-1ubuntu1) ... 345s Selecting previously unselected package libsz2:amd64. 345s Preparing to unpack .../05-libsz2_1.1.3-1_amd64.deb ... 345s Unpacking libsz2:amd64 (1.1.3-1) ... 345s Selecting previously unselected package libhdf5-310:amd64. 345s Preparing to unpack .../06-libhdf5-310_1.14.5+repack-3_amd64.deb ... 345s Unpacking libhdf5-310:amd64 (1.14.5+repack-3) ... 345s Selecting previously unselected package libhdf5-hl-310:amd64. 345s Preparing to unpack .../07-libhdf5-hl-310_1.14.5+repack-3_amd64.deb ... 345s Unpacking libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 346s Selecting previously unselected package liblapack3:amd64. 346s Preparing to unpack .../08-liblapack3_3.12.1-2_amd64.deb ... 346s Unpacking liblapack3:amd64 (3.12.1-2) ... 346s Selecting previously unselected package liblbfgsb0:amd64. 346s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 346s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 346s Selecting previously unselected package liblzf1:amd64. 346s Preparing to unpack .../10-liblzf1_3.6-4_amd64.deb ... 346s Unpacking liblzf1:amd64 (3.6-4) ... 346s Selecting previously unselected package python3-all. 346s Preparing to unpack .../11-python3-all_3.13.1-1~exp2_amd64.deb ... 346s Unpacking python3-all (3.13.1-1~exp2) ... 346s Selecting previously unselected package python3-numpy. 346s Preparing to unpack .../12-python3-numpy_1%3a1.26.4+ds-13_amd64.deb ... 346s Unpacking python3-numpy (1:1.26.4+ds-13) ... 346s Selecting previously unselected package python3-h5py-serial. 346s Preparing to unpack .../13-python3-h5py-serial_3.12.1-1_amd64.deb ... 346s Unpacking python3-h5py-serial (3.12.1-1) ... 346s Selecting previously unselected package python3-h5py. 346s Preparing to unpack .../14-python3-h5py_3.12.1-1_all.deb ... 346s Unpacking python3-h5py (3.12.1-1) ... 346s Selecting previously unselected package python3-click. 346s Preparing to unpack .../15-python3-click_8.1.8-1_all.deb ... 346s Unpacking python3-click (8.1.8-1) ... 346s Selecting previously unselected package python3-dateutil. 346s Preparing to unpack .../16-python3-dateutil_2.9.0-3_all.deb ... 346s Unpacking python3-dateutil (2.9.0-3) ... 346s Selecting previously unselected package python3-pytz. 346s Preparing to unpack .../17-python3-pytz_2025.1-3_all.deb ... 346s Unpacking python3-pytz (2025.1-3) ... 346s Selecting previously unselected package python3-tz. 346s Preparing to unpack .../18-python3-tz_2025.1-3_all.deb ... 346s Unpacking python3-tz (2025.1-3) ... 346s Selecting previously unselected package python3-pandas-lib:amd64. 346s Preparing to unpack .../19-python3-pandas-lib_2.2.3+dfsg-8_amd64.deb ... 346s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 347s Selecting previously unselected package python3-pandas. 347s Preparing to unpack .../20-python3-pandas_2.2.3+dfsg-8_all.deb ... 347s Unpacking python3-pandas (2.2.3+dfsg-8) ... 347s Selecting previously unselected package python3-decorator. 347s Preparing to unpack .../21-python3-decorator_5.1.1-5_all.deb ... 347s Unpacking python3-decorator (5.1.1-5) ... 347s Selecting previously unselected package python3-scipy. 347s Preparing to unpack .../22-python3-scipy_1.14.1-4ubuntu1_amd64.deb ... 347s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 348s Selecting previously unselected package python3-biom-format. 348s Preparing to unpack .../23-python3-biom-format_2.1.16-1build2_amd64.deb ... 348s Unpacking python3-biom-format (2.1.16-1build2) ... 348s Setting up python3.12-minimal (3.12.9-1) ... 349s Setting up python3.12 (3.12.9-1) ... 350s Setting up python3-all (3.13.1-1~exp2) ... 350s Setting up python3-pytz (2025.1-3) ... 350s Setting up python3-click (8.1.8-1) ... 350s Setting up libaec0:amd64 (1.1.3-1) ... 350s Setting up python3-tz (2025.1-3) ... 350s Setting up python3-decorator (5.1.1-5) ... 351s Setting up libblas3:amd64 (3.12.1-2) ... 351s 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 351s Setting up liblzf1:amd64 (3.6-4) ... 351s Setting up libgfortran5:amd64 (15-20250213-1ubuntu1) ... 351s Setting up python3-dateutil (2.9.0-3) ... 351s Setting up libsz2:amd64 (1.1.3-1) ... 351s Setting up liblapack3:amd64 (3.12.1-2) ... 351s 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 351s Setting up python3-numpy (1:1.26.4+ds-13) ... 354s Setting up libhdf5-310:amd64 (1.14.5+repack-3) ... 354s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 354s Setting up libhdf5-hl-310:amd64 (1.14.5+repack-3) ... 354s Setting up python3-scipy (1.14.1-4ubuntu1) ... 361s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-8) ... 361s Setting up python3-h5py-serial (3.12.1-1) ... 361s Setting up python3-pandas (2.2.3+dfsg-8) ... 371s Setting up python3-h5py (3.12.1-1) ... 371s Setting up python3-biom-format (2.1.16-1build2) ... 371s Processing triggers for systemd (257.2-3ubuntu1) ... 371s Processing triggers for man-db (2.13.0-1) ... 372s Processing triggers for libc-bin (2.40-4ubuntu1) ... 377s autopkgtest [13:21:31]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import biom; print(biom)" ; done 377s autopkgtest [13:21:31]: test autodep8-python3: [----------------------- 378s Testing with python3.12: 379s 379s Testing with python3.13: 379s 380s autopkgtest [13:21:34]: test autodep8-python3: -----------------------] 380s autopkgtest [13:21:34]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 380s autodep8-python3 PASS (superficial) 381s autopkgtest [13:21:35]: @@@@@@@@@@@@@@@@@@@@ summary 381s run-unit-test PASS 381s autodep8-python3 PASS (superficial) 399s nova [W] Skipping flock for amd64 399s Creating nova instance adt-plucky-amd64-python-biom-format-20250219-131514-juju-7f2275-prod-proposed-migration-environment-2-dc851108-dc3a-4b55-b63d-704a90221ce3 from image adt/ubuntu-plucky-amd64-server-20250219.img (UUID 90711abf-916f-4a80-845a-825250a78697)... 399s nova [W] Timed out waiting for 64967d9d-3cde-4b34-876e-f17da883a644 to get deleted. 399s nova [W] Skipping flock for amd64 399s Creating nova instance adt-plucky-amd64-python-biom-format-20250219-131514-juju-7f2275-prod-proposed-migration-environment-2-dc851108-dc3a-4b55-b63d-704a90221ce3 from image adt/ubuntu-plucky-amd64-server-20250219.img (UUID 90711abf-916f-4a80-845a-825250a78697)... 399s nova [W] Timed out waiting for d71a52c7-dd5a-4fd3-9bdf-b006d90001cd to get deleted.