0s autopkgtest [17:34:17]: starting date and time: 2025-03-15 17:34:17+0000 0s autopkgtest [17:34:17]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [17:34:17]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.prlj49_x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.41-1ubuntu2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-11.secgroup --name adt-plucky-s390x-python-biom-format-20250315-170915-juju-7f2275-prod-proposed-migration-environment-20-49474468-5e0d-40a4-b18d-ea2f59d9d1ea --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-s390x -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/ 139s autopkgtest [17:36:36]: testbed dpkg architecture: s390x 140s autopkgtest [17:36:37]: testbed apt version: 2.9.33 140s autopkgtest [17:36:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 140s autopkgtest [17:36:37]: testbed release detected to be: None 141s autopkgtest [17:36:38]: updating testbed package index (apt update) 141s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 142s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 142s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 142s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 142s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 142s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 142s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 142s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 143s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 143s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 143s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 143s Fetched 1073 kB in 2s (679 kB/s) 143s Reading package lists... 144s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Calculating upgrade... 144s Calculating upgrade... 144s The following packages were automatically installed and are no longer required: 144s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 144s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 144s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 144s linux-tools-6.11.0-8-generic 144s Use 'sudo apt autoremove' to remove them. 144s The following packages will be upgraded: 144s pinentry-curses python3-jinja2 strace 144s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 652 kB of archives. 144s After this operation, 27.6 kB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 145s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 145s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 146s Fetched 652 kB in 1s (605 kB/s) 146s (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 ... 81428 files and directories currently installed.) 146s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 146s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 146s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 146s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 146s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 146s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 146s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 146s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 146s Setting up strace (6.13+ds-1ubuntu1) ... 146s Processing triggers for man-db (2.13.0-1) ... 147s Reading package lists... 147s Building dependency tree... 147s Reading state information... 147s Solving dependencies... 147s The following packages will be REMOVED: 147s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 147s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 147s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 147s linux-tools-6.11.0-8-generic* 147s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 147s After this operation, 167 MB disk space will be freed. 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 ... 81428 files and directories currently installed.) 147s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 147s Removing libpython3.12t64:s390x (3.12.9-1) ... 147s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 147s Removing libnsl2:s390x (1.3.0-3build3) ... 147s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 147s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 147s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 148s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s Processing triggers for libc-bin (2.41-1ubuntu1) ... 148s (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 ... 56328 files and directories currently installed.) 148s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 148s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 148s autopkgtest [17:36:45]: upgrading testbed (apt dist-upgrade and autopurge) 148s Reading package lists... 149s Building dependency tree... 149s Reading state information... 149s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 149s Starting 2 pkgProblemResolver with broken count: 0 149s Done 149s Entering ResolveByKeep 149s 149s Calculating upgrade... 149s The following packages will be upgraded: 149s libc-bin libc-dev-bin libc6 libc6-dev locales 149s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 149s Need to get 9512 kB of archives. 149s After this operation, 8192 B of additional disk space will be used. 149s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 151s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 151s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 154s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 154s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 159s Preconfiguring packages ... 159s Fetched 9512 kB in 9s (1017 kB/s) 159s (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 ... 56326 files and directories currently installed.) 159s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 159s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 159s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 159s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up libc6:s390x (2.41-1ubuntu2) ... 159s (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 ... 56326 files and directories currently installed.) 159s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 159s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up libc-bin (2.41-1ubuntu2) ... 159s (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 ... 56326 files and directories currently installed.) 159s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 159s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 159s Setting up locales (2.41-1ubuntu2) ... 160s Generating locales (this might take a while)... 161s en_US.UTF-8... done 161s Generation complete. 161s Setting up libc-dev-bin (2.41-1ubuntu2) ... 161s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 161s Processing triggers for man-db (2.13.0-1) ... 161s Processing triggers for systemd (257.3-1ubuntu3) ... 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 162s Starting pkgProblemResolver with broken count: 0 162s Starting 2 pkgProblemResolver with broken count: 0 162s Done 162s Solving dependencies... 162s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 163s autopkgtest [17:37:00]: rebooting testbed after setup commands that affected boot 181s autopkgtest [17:37:18]: testbed running kernel: Linux 6.14.0-10-generic #10-Ubuntu SMP Wed Mar 12 14:53:49 UTC 2025 183s autopkgtest [17:37:20]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 197s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (dsc) [2498 B] 197s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (tar) [11.9 MB] 197s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build3 (diff) [11.7 kB] 197s gpgv: Signature made Tue Mar 4 15:18:02 2025 UTC 197s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 197s gpgv: Can't check signature: No public key 197s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build3.dsc: no acceptable signature found 198s autopkgtest [17:37:35]: testing package python-biom-format version 2.1.16-1build3 199s autopkgtest [17:37:36]: build not needed 202s autopkgtest [17:37:39]: test run-unit-test: preparing testbed 202s Reading package lists... 202s Building dependency tree... 202s Reading state information... 202s Starting pkgProblemResolver with broken count: 0 202s Starting 2 pkgProblemResolver with broken count: 0 202s Done 203s The following NEW packages will be installed: 203s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 libjs-jquery 203s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 203s python-biom-format-doc python3-biom-format python3-click python3-dateutil 203s python3-decorator python3-h5py python3-h5py-serial python3-numpy 203s python3-numpy-dev python3-pandas python3-pandas-lib python3-pytz 203s python3-scipy python3-tz 203s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 203s Need to get 38.3 MB of archives. 203s After this operation, 165 MB of additional disk space will be used. 203s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 203s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 203s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 204s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 207s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 211s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 211s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 211s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 212s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 212s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 213s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 213s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 8.1.3-4 [30.9 kB] 213s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 213s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 213s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biom-format-doc all 2.1.16-1build3 [57.5 kB] 213s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.13.0-1 [1185 kB] 214s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.13.0-1 [7978 B] 214s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 214s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 214s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pytz all 2025.1-3 [162 kB] 215s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2025.1-3 [1866 B] 215s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-8build1 [4995 kB] 220s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 223s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 223s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 241s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1build3 [150 kB] 241s Fetched 38.3 MB in 38s (999 kB/s) 241s Selecting previously unselected package python3-numpy-dev:s390x. 241s (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 ... 56326 files and directories currently installed.) 241s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 241s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 241s Selecting previously unselected package libblas3:s390x. 241s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 241s Unpacking libblas3:s390x (3.12.1-2) ... 241s Selecting previously unselected package libgfortran5:s390x. 241s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 241s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 241s Selecting previously unselected package liblapack3:s390x. 241s Preparing to unpack .../03-liblapack3_3.12.1-2_s390x.deb ... 241s Unpacking liblapack3:s390x (3.12.1-2) ... 241s Selecting previously unselected package python3-numpy. 241s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 241s Unpacking python3-numpy (1:2.2.3+ds-5) ... 242s Selecting previously unselected package libaec0:s390x. 242s Preparing to unpack .../05-libaec0_1.1.3-1_s390x.deb ... 242s Unpacking libaec0:s390x (1.1.3-1) ... 242s Selecting previously unselected package libsz2:s390x. 242s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 242s Unpacking libsz2:s390x (1.1.3-1) ... 242s Selecting previously unselected package libhdf5-310:s390x. 242s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_s390x.deb ... 242s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 242s Selecting previously unselected package libhdf5-hl-310:s390x. 242s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 242s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 242s Selecting previously unselected package libjs-jquery. 242s Preparing to unpack .../09-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 242s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 242s Selecting previously unselected package libjs-underscore. 242s Preparing to unpack .../10-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 242s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 242s Selecting previously unselected package libjs-sphinxdoc. 242s Preparing to unpack .../11-libjs-sphinxdoc_8.1.3-4_all.deb ... 242s Unpacking libjs-sphinxdoc (8.1.3-4) ... 242s Selecting previously unselected package liblbfgsb0:s390x. 242s Preparing to unpack .../12-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 242s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 242s Selecting previously unselected package liblzf1:s390x. 242s Preparing to unpack .../13-liblzf1_3.6-4_s390x.deb ... 242s Unpacking liblzf1:s390x (3.6-4) ... 242s Selecting previously unselected package python-biom-format-doc. 242s Preparing to unpack .../14-python-biom-format-doc_2.1.16-1build3_all.deb ... 242s Unpacking python-biom-format-doc (2.1.16-1build3) ... 242s Selecting previously unselected package python3-h5py-serial. 242s Preparing to unpack .../15-python3-h5py-serial_3.13.0-1_s390x.deb ... 242s Unpacking python3-h5py-serial (3.13.0-1) ... 242s Selecting previously unselected package python3-h5py. 242s Preparing to unpack .../16-python3-h5py_3.13.0-1_all.deb ... 242s Unpacking python3-h5py (3.13.0-1) ... 242s Selecting previously unselected package python3-click. 242s Preparing to unpack .../17-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 242s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 242s Selecting previously unselected package python3-dateutil. 242s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 242s Unpacking python3-dateutil (2.9.0-3) ... 242s Selecting previously unselected package python3-pytz. 242s Preparing to unpack .../19-python3-pytz_2025.1-3_all.deb ... 242s Unpacking python3-pytz (2025.1-3) ... 242s Selecting previously unselected package python3-tz. 242s Preparing to unpack .../20-python3-tz_2025.1-3_all.deb ... 242s Unpacking python3-tz (2025.1-3) ... 242s Selecting previously unselected package python3-pandas-lib:s390x. 242s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-8build1_s390x.deb ... 242s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-8build1) ... 242s Selecting previously unselected package python3-pandas. 242s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 242s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 242s Selecting previously unselected package python3-decorator. 242s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ... 242s Unpacking python3-decorator (5.1.1-5) ... 242s Selecting previously unselected package python3-scipy. 242s Preparing to unpack .../24-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 242s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 242s Selecting previously unselected package python3-biom-format. 242s Preparing to unpack .../25-python3-biom-format_2.1.16-1build3_s390x.deb ... 242s Unpacking python3-biom-format (2.1.16-1build3) ... 242s Setting up python3-pytz (2025.1-3) ... 242s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 243s Setting up libaec0:s390x (1.1.3-1) ... 243s Setting up python3-tz (2025.1-3) ... 243s Setting up python3-decorator (5.1.1-5) ... 243s Setting up libblas3:s390x (3.12.1-2) ... 243s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 243s Setting up liblzf1:s390x (3.6-4) ... 243s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 243s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 243s Setting up python3-dateutil (2.9.0-3) ... 243s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 243s Setting up libsz2:s390x (1.1.3-1) ... 243s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 243s Setting up liblapack3:s390x (3.12.1-2) ... 243s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 243s Setting up python3-numpy (1:2.2.3+ds-5) ... 244s Setting up libjs-sphinxdoc (8.1.3-4) ... 244s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 244s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 244s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 244s Setting up python3-scipy (1.14.1-4ubuntu2) ... 246s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-8build1) ... 246s Setting up python3-h5py-serial (3.13.0-1) ... 246s Setting up python-biom-format-doc (2.1.16-1build3) ... 246s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 250s Setting up python3-h5py (3.13.0-1) ... 250s Setting up python3-biom-format (2.1.16-1build3) ... 250s Processing triggers for man-db (2.13.0-1) ... 250s Processing triggers for libc-bin (2.41-1ubuntu2) ... 251s autopkgtest [17:38:28]: test run-unit-test: [----------------------- 252s 252s System information 252s ================== 252s Platform: linux 252s Python version: 3.13.2 (main, Mar 13 2025, 14:29:07) [GCC 14.2.0] 252s Python executable: /usr/bin/python3 252s 252s Dependency versions 252s =================== 252s click version: 8.1.8 252s NumPy version: 2.2.3 252s SciPy version: 1.14.1 252s h5py version: 3.13.0 252s 252s biom-format package information 252s =============================== 252s biom-format version: 2.1.16 252s 253s 253s The input file is a valid BIOM-formatted file. 253s 253s The input file is a valid BIOM-formatted file. 254s 254s The input file is a valid BIOM-formatted file. 254s 254s The input file is a valid BIOM-formatted file. 255s + table=examples/min_sparse_otu_table_hdf5.biom 255s + obsmd=examples/obs_md.txt 255s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 255s + biom show-install-info 256s 256s System information 256s ================== 256s Platform: linux 256s Python version: 3.13.2 (main, Mar 13 2025, 14:29:07) [GCC 14.2.0] 256s Python executable: /usr/bin/python3 256s 256s Dependency versions 256s =================== 256s click version: 8.1.8 256s NumPy version: 2.2.3 256s SciPy version: 1.14.1 256s h5py version: 3.13.0 256s 256s biom-format package information 256s =============================== 256s biom-format version: 2.1.16 256s 256s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 256s 256s The input file is a valid BIOM-formatted file. 256s + 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 257s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 257s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 258s + biom validate-table -i test_json.biom 258s 258s The input file is a valid BIOM-formatted file. 258s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 259s + biom validate-table -i test_hdf5.biom 259s 259s The input file is a valid BIOM-formatted file. 260s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 260s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 261s + biom validate-table -i test_hdf5.biom 261s 261s The input file is a valid BIOM-formatted file. 261s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 262s + biom validate-table -i test_json.biom 262s 262s The input file is a valid BIOM-formatted file. 262s + biom head -i examples/min_sparse_otu_table_hdf5.biom 263s # Constructed from biom file 263s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 263s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 263s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 263s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 263s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 263s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 263s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 263s Sample1 263s Sample2 263s Sample3 263s Sample4 263s Sample5 263s Sample6 263s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 264s + cat 264s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 264s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 265s Num samples: 6 265s Num observations: 5 265s Total count: 27 265s Table density (fraction of non-zero values): 0.500 265s 265s Counts/sample summary: 265s Min: 3.000 265s Max: 7.000 265s Median: 4.000 265s Mean: 4.500 265s Std. dev.: 1.500 265s Sample Metadata Categories: None provided 265s Observation Metadata Categories: None provided 265s 265s Counts/sample detail: 265s Sample2: 3.000 265s Sample5: 3.000 265s Sample3: 4.000 265s Sample6: 4.000 265s Sample4: 6.000 265s Sample1: 7.000 265s + cat 265s + biom from-uc -i uctest -o test_uc.biom 265s If this message was shown, then all commands executed without failure 265s + echo If this message was shown, then all commands executed without failure 265s autopkgtest [17:38:42]: test run-unit-test: -----------------------] 266s autopkgtest [17:38:43]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 266s run-unit-test PASS 266s autopkgtest [17:38:43]: test autodep8-python3: preparing testbed 419s autopkgtest [17:41:16]: testbed dpkg architecture: s390x 419s autopkgtest [17:41:16]: testbed apt version: 2.9.33 419s autopkgtest [17:41:16]: @@@@@@@@@@@@@@@@@@@@ test bed setup 420s autopkgtest [17:41:17]: testbed release detected to be: plucky 420s autopkgtest [17:41:17]: updating testbed package index (apt update) 421s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 421s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 421s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 421s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 421s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [99.7 kB] 421s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.8 kB] 421s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [379 kB] 421s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [113 kB] 421s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x c-n-f Metadata [1824 B] 421s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x c-n-f Metadata [116 B] 421s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [320 kB] 422s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x c-n-f Metadata [13.4 kB] 422s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3776 B] 422s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x c-n-f Metadata [240 B] 422s Fetched 1073 kB in 1s (756 kB/s) 423s Reading package lists... 423s Reading package lists... 423s Building dependency tree... 423s Reading state information... 423s Calculating upgrade... 423s Calculating upgrade... 423s The following packages were automatically installed and are no longer required: 423s libnsl2 libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 423s linux-headers-6.11.0-8 linux-headers-6.11.0-8-generic 423s linux-modules-6.11.0-8-generic linux-tools-6.11.0-8 423s linux-tools-6.11.0-8-generic 423s Use 'sudo apt autoremove' to remove them. 423s The following packages will be upgraded: 423s pinentry-curses python3-jinja2 strace 424s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 424s Need to get 652 kB of archives. 424s After this operation, 27.6 kB of additional disk space will be used. 424s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x strace s390x 6.13+ds-1ubuntu1 [500 kB] 424s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x pinentry-curses s390x 1.3.1-2ubuntu3 [42.9 kB] 424s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 425s Fetched 652 kB in 1s (691 kB/s) 425s (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 ... 81428 files and directories currently installed.) 425s Preparing to unpack .../strace_6.13+ds-1ubuntu1_s390x.deb ... 425s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 425s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_s390x.deb ... 425s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 425s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 425s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 425s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 425s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 425s Setting up strace (6.13+ds-1ubuntu1) ... 425s Processing triggers for man-db (2.13.0-1) ... 426s Reading package lists... 426s Building dependency tree... 426s Reading state information... 426s Solving dependencies... 426s The following packages will be REMOVED: 426s libnsl2* libpython3.12-minimal* libpython3.12-stdlib* libpython3.12t64* 426s linux-headers-6.11.0-8* linux-headers-6.11.0-8-generic* 426s linux-modules-6.11.0-8-generic* linux-tools-6.11.0-8* 426s linux-tools-6.11.0-8-generic* 426s 0 upgraded, 0 newly installed, 9 to remove and 5 not upgraded. 426s After this operation, 167 MB disk space will be freed. 426s (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 ... 81428 files and directories currently installed.) 426s Removing linux-tools-6.11.0-8-generic (6.11.0-8.8) ... 426s Removing linux-tools-6.11.0-8 (6.11.0-8.8) ... 426s Removing libpython3.12t64:s390x (3.12.9-1) ... 426s Removing libpython3.12-stdlib:s390x (3.12.9-1) ... 426s Removing libnsl2:s390x (1.3.0-3build3) ... 426s Removing libpython3.12-minimal:s390x (3.12.9-1) ... 426s Removing linux-headers-6.11.0-8-generic (6.11.0-8.8) ... 426s Removing linux-headers-6.11.0-8 (6.11.0-8.8) ... 427s Removing linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 427s Processing triggers for libc-bin (2.41-1ubuntu1) ... 427s (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 ... 56328 files and directories currently installed.) 427s Purging configuration files for libpython3.12-minimal:s390x (3.12.9-1) ... 427s Purging configuration files for linux-modules-6.11.0-8-generic (6.11.0-8.8) ... 427s autopkgtest [17:41:24]: upgrading testbed (apt dist-upgrade and autopurge) 427s Reading package lists... 428s Building dependency tree... 428s Reading state information... 428s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 428s Starting 2 pkgProblemResolver with broken count: 0 428s Done 428s Entering ResolveByKeep 428s 428s Calculating upgrade... 428s The following packages will be upgraded: 428s libc-bin libc-dev-bin libc6 libc6-dev locales 428s 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 428s Need to get 9512 kB of archives. 428s After this operation, 8192 B of additional disk space will be used. 428s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6-dev s390x 2.41-1ubuntu2 [1678 kB] 430s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-dev-bin s390x 2.41-1ubuntu2 [24.3 kB] 430s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc6 s390x 2.41-1ubuntu2 [2892 kB] 432s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libc-bin s390x 2.41-1ubuntu2 [671 kB] 432s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x locales all 2.41-1ubuntu2 [4246 kB] 435s Preconfiguring packages ... 435s Fetched 9512 kB in 7s (1460 kB/s) 435s (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 ... 56326 files and directories currently installed.) 435s Preparing to unpack .../libc6-dev_2.41-1ubuntu2_s390x.deb ... 435s Unpacking libc6-dev:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 435s Preparing to unpack .../libc-dev-bin_2.41-1ubuntu2_s390x.deb ... 435s Unpacking libc-dev-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 435s Preparing to unpack .../libc6_2.41-1ubuntu2_s390x.deb ... 435s Unpacking libc6:s390x (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 435s Setting up libc6:s390x (2.41-1ubuntu2) ... 435s (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 ... 56326 files and directories currently installed.) 435s Preparing to unpack .../libc-bin_2.41-1ubuntu2_s390x.deb ... 435s Unpacking libc-bin (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 435s Setting up libc-bin (2.41-1ubuntu2) ... 435s (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 ... 56326 files and directories currently installed.) 435s Preparing to unpack .../locales_2.41-1ubuntu2_all.deb ... 435s Unpacking locales (2.41-1ubuntu2) over (2.41-1ubuntu1) ... 436s Setting up locales (2.41-1ubuntu2) ... 436s Generating locales (this might take a while)... 437s en_US.UTF-8... done 437s Generation complete. 437s Setting up libc-dev-bin (2.41-1ubuntu2) ... 437s Setting up libc6-dev:s390x (2.41-1ubuntu2) ... 437s Processing triggers for man-db (2.13.0-1) ... 437s Processing triggers for systemd (257.3-1ubuntu3) ... 438s Reading package lists... 438s Building dependency tree... 438s Reading state information... 439s Starting pkgProblemResolver with broken count: 0 439s Starting 2 pkgProblemResolver with broken count: 0 439s Done 439s Solving dependencies... 439s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 439s autopkgtest [17:41:36]: rebooting testbed after setup commands that affected boot 460s Reading package lists... 460s Building dependency tree... 460s Reading state information... 460s Starting pkgProblemResolver with broken count: 0 460s Starting 2 pkgProblemResolver with broken count: 0 460s Done 460s The following NEW packages will be installed: 460s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 460s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 460s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 460s python3-numpy python3-numpy-dev python3-pandas python3-pandas-lib 460s python3-pytz python3-scipy python3-tz 460s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 460s Need to get 37.7 MB of archives. 460s After this operation, 163 MB of additional disk space will be used. 460s Get:1 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy-dev s390x 1:2.2.3+ds-5 [147 kB] 461s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.1-2 [252 kB] 461s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 15-20250222-0ubuntu1 [620 kB] 461s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.1-2 [2971 kB] 464s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:2.2.3+ds-5 [4396 kB] 467s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 467s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 467s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-310 s390x 1.14.5+repack-3 [1477 kB] 468s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-310 s390x 1.14.5+repack-3 [61.0 kB] 468s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 468s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 468s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.13.2-2 [886 B] 468s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.13.0-1 [1185 kB] 469s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.13.0-1 [7978 B] 469s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 469s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 469s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-pytz all 2025.1-3 [162 kB] 469s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2025.1-3 [1866 B] 469s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-8build1 [4995 kB] 471s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-8build1 [3112 kB] 473s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 473s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.14.1-4ubuntu2 [18.0 MB] 481s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1build3 [150 kB] 481s Fetched 37.7 MB in 21s (1805 kB/s) 481s Selecting previously unselected package python3-numpy-dev:s390x. 482s (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 ... 56326 files and directories currently installed.) 482s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_s390x.deb ... 482s Unpacking python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 482s Selecting previously unselected package libblas3:s390x. 482s Preparing to unpack .../01-libblas3_3.12.1-2_s390x.deb ... 482s Unpacking libblas3:s390x (3.12.1-2) ... 482s Selecting previously unselected package libgfortran5:s390x. 482s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_s390x.deb ... 482s Unpacking libgfortran5:s390x (15-20250222-0ubuntu1) ... 482s Selecting previously unselected package liblapack3:s390x. 482s Preparing to unpack .../03-liblapack3_3.12.1-2_s390x.deb ... 482s Unpacking liblapack3:s390x (3.12.1-2) ... 482s Selecting previously unselected package python3-numpy. 482s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_s390x.deb ... 482s Unpacking python3-numpy (1:2.2.3+ds-5) ... 482s Selecting previously unselected package libaec0:s390x. 482s Preparing to unpack .../05-libaec0_1.1.3-1_s390x.deb ... 482s Unpacking libaec0:s390x (1.1.3-1) ... 482s Selecting previously unselected package libsz2:s390x. 482s Preparing to unpack .../06-libsz2_1.1.3-1_s390x.deb ... 482s Unpacking libsz2:s390x (1.1.3-1) ... 482s Selecting previously unselected package libhdf5-310:s390x. 482s Preparing to unpack .../07-libhdf5-310_1.14.5+repack-3_s390x.deb ... 482s Unpacking libhdf5-310:s390x (1.14.5+repack-3) ... 482s Selecting previously unselected package libhdf5-hl-310:s390x. 482s Preparing to unpack .../08-libhdf5-hl-310_1.14.5+repack-3_s390x.deb ... 482s Unpacking libhdf5-hl-310:s390x (1.14.5+repack-3) ... 482s Selecting previously unselected package liblbfgsb0:s390x. 482s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 482s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 482s Selecting previously unselected package liblzf1:s390x. 482s Preparing to unpack .../10-liblzf1_3.6-4_s390x.deb ... 482s Unpacking liblzf1:s390x (3.6-4) ... 482s Selecting previously unselected package python3-all. 482s Preparing to unpack .../11-python3-all_3.13.2-2_s390x.deb ... 482s Unpacking python3-all (3.13.2-2) ... 482s Selecting previously unselected package python3-h5py-serial. 482s Preparing to unpack .../12-python3-h5py-serial_3.13.0-1_s390x.deb ... 482s Unpacking python3-h5py-serial (3.13.0-1) ... 482s Selecting previously unselected package python3-h5py. 482s Preparing to unpack .../13-python3-h5py_3.13.0-1_all.deb ... 482s Unpacking python3-h5py (3.13.0-1) ... 482s Selecting previously unselected package python3-click. 482s Preparing to unpack .../14-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 482s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 482s Selecting previously unselected package python3-dateutil. 482s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 482s Unpacking python3-dateutil (2.9.0-3) ... 482s Selecting previously unselected package python3-pytz. 482s Preparing to unpack .../16-python3-pytz_2025.1-3_all.deb ... 482s Unpacking python3-pytz (2025.1-3) ... 482s Selecting previously unselected package python3-tz. 482s Preparing to unpack .../17-python3-tz_2025.1-3_all.deb ... 482s Unpacking python3-tz (2025.1-3) ... 482s Selecting previously unselected package python3-pandas-lib:s390x. 482s Preparing to unpack .../18-python3-pandas-lib_2.2.3+dfsg-8build1_s390x.deb ... 482s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-8build1) ... 482s Selecting previously unselected package python3-pandas. 482s Preparing to unpack .../19-python3-pandas_2.2.3+dfsg-8build1_all.deb ... 482s Unpacking python3-pandas (2.2.3+dfsg-8build1) ... 482s Selecting previously unselected package python3-decorator. 482s Preparing to unpack .../20-python3-decorator_5.1.1-5_all.deb ... 482s Unpacking python3-decorator (5.1.1-5) ... 482s Selecting previously unselected package python3-scipy. 482s Preparing to unpack .../21-python3-scipy_1.14.1-4ubuntu2_s390x.deb ... 482s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 482s Selecting previously unselected package python3-biom-format. 482s Preparing to unpack .../22-python3-biom-format_2.1.16-1build3_s390x.deb ... 482s Unpacking python3-biom-format (2.1.16-1build3) ... 482s Setting up python3-all (3.13.2-2) ... 482s Setting up python3-pytz (2025.1-3) ... 483s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 483s Setting up libaec0:s390x (1.1.3-1) ... 483s Setting up python3-tz (2025.1-3) ... 483s Setting up python3-decorator (5.1.1-5) ... 483s Setting up libblas3:s390x (3.12.1-2) ... 483s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 483s Setting up liblzf1:s390x (3.6-4) ... 483s Setting up python3-numpy-dev:s390x (1:2.2.3+ds-5) ... 483s Setting up libgfortran5:s390x (15-20250222-0ubuntu1) ... 483s Setting up python3-dateutil (2.9.0-3) ... 483s Setting up libsz2:s390x (1.1.3-1) ... 483s Setting up liblapack3:s390x (3.12.1-2) ... 483s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 483s Setting up python3-numpy (1:2.2.3+ds-5) ... 484s Setting up libhdf5-310:s390x (1.14.5+repack-3) ... 484s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 484s Setting up libhdf5-hl-310:s390x (1.14.5+repack-3) ... 484s Setting up python3-scipy (1.14.1-4ubuntu2) ... 486s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-8build1) ... 486s Setting up python3-h5py-serial (3.13.0-1) ... 487s Setting up python3-pandas (2.2.3+dfsg-8build1) ... 490s Setting up python3-h5py (3.13.0-1) ... 490s Setting up python3-biom-format (2.1.16-1build3) ... 490s Processing triggers for man-db (2.13.0-1) ... 490s Processing triggers for libc-bin (2.41-1ubuntu2) ... 495s autopkgtest [17:42:32]: 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 495s autopkgtest [17:42:32]: test autodep8-python3: [----------------------- 495s Testing with python3.13: 496s 496s autopkgtest [17:42:33]: test autodep8-python3: -----------------------] 497s autopkgtest [17:42:34]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 497s autodep8-python3 PASS (superficial) 497s autopkgtest [17:42:34]: @@@@@@@@@@@@@@@@@@@@ summary 497s run-unit-test PASS 497s autodep8-python3 PASS (superficial) 515s nova [W] Using flock in prodstack6-s390x 515s Creating nova instance adt-plucky-s390x-python-biom-format-20250315-170915-juju-7f2275-prod-proposed-migration-environment-20-49474468-5e0d-40a4-b18d-ea2f59d9d1ea from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 515s nova [W] Timed out waiting for 1176064d-2b4a-448a-8041-3ea9fe4c6e84 to get deleted. 515s nova [W] Using flock in prodstack6-s390x 515s Creating nova instance adt-plucky-s390x-python-biom-format-20250315-170915-juju-7f2275-prod-proposed-migration-environment-20-49474468-5e0d-40a4-b18d-ea2f59d9d1ea from image adt/ubuntu-plucky-s390x-server-20250315.img (UUID 3d3557fa-fd0f-4bba-9b89-8d5964e09f61)... 515s nova [W] Timed out waiting for 8fc07858-baae-41b3-96de-615361bd9ec4 to get deleted.