0s autopkgtest [14:37:39]: starting date and time: 2024-12-04 14:37:39+0000 0s autopkgtest [14:37:39]: git checkout: 48af33f0 Fix --add-apt-source=ppa for focal 0s autopkgtest [14:37:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pq1ull21/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:openmpi --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu3 openmpi/5.0.6-3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-29.secgroup --name adt-plucky-s390x-python-biom-format-20241204-143739-juju-7f2275-prod-proposed-migration-environment-20-19d430af-d9bc-4a4b-a911-7bb392784037 --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'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 122s autopkgtest [14:39:41]: testbed dpkg architecture: s390x 122s autopkgtest [14:39:41]: testbed apt version: 2.9.16 122s autopkgtest [14:39:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 122s autopkgtest [14:39:41]: testbed release detected to be: None 123s autopkgtest [14:39:42]: updating testbed package index (apt update) 123s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 123s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 124s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 124s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 124s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.2 kB] 124s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [745 kB] 124s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 124s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [58.3 kB] 124s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [106 kB] 124s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [928 B] 124s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [578 kB] 124s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [7444 B] 124s Fetched 1593 kB in 1s (1712 kB/s) 125s Reading package lists... 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 125s Calculating upgrade... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 126s autopkgtest [14:39:45]: upgrading testbed (apt dist-upgrade and autopurge) 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 127s Entering ResolveByKeep 127s 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [14:39:49]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 130s autopkgtest [14:39:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 132s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (dsc) [2498 B] 132s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (tar) [11.9 MB] 132s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (diff) [11.6 kB] 132s gpgv: Signature made Fri Nov 15 13:41:43 2024 UTC 132s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build1.dsc: no acceptable signature found 133s autopkgtest [14:39:52]: testing package python-biom-format version 2.1.16-1build1 133s autopkgtest [14:39:52]: build not needed 136s autopkgtest [14:39:55]: test run-unit-test: preparing testbed 136s Reading package lists... 137s Building dependency tree... 137s Reading state information... 137s Starting pkgProblemResolver with broken count: 0 137s Starting 2 pkgProblemResolver with broken count: 0 137s Done 137s The following NEW packages will be installed: 137s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 137s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 137s libsz2 python-biom-format-doc python3-biom-format python3-click 137s python3-colorama python3-dateutil python3-decorator python3-h5py 137s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 137s python3-scipy python3-tz 137s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 137s Need to get 44.5 MB of archives. 137s After this operation, 236 MB of additional disk space will be used. 137s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 137s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-4 [238 kB] 137s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-9ubuntu1 [587 kB] 137s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 137s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 138s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 138s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 138s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 138s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 138s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-4 [2964 kB] 138s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 138s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 138s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biom-format-doc all 2.1.16-1build1 [57.9 kB] 138s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 138s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py-serial s390x 3.11.0-8ubuntu3 [1655 kB] 138s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py all 3.11.0-8ubuntu3 [7982 B] 138s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 138s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB] 138s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 138s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 138s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5ubuntu1 [8010 kB] 138s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 138s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 138s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5ubuntu1 [20.7 MB] 139s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1build1 [178 kB] 139s Fetched 44.5 MB in 2s (24.3 MB/s) 139s Selecting previously unselected package libaec0:s390x. 139s (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 ... 55869 files and directories currently installed.) 139s Preparing to unpack .../00-libaec0_1.1.3-1_s390x.deb ... 139s Unpacking libaec0:s390x (1.1.3-1) ... 139s Selecting previously unselected package libblas3:s390x. 139s Preparing to unpack .../01-libblas3_3.12.0-4_s390x.deb ... 139s Unpacking libblas3:s390x (3.12.0-4) ... 139s Selecting previously unselected package libgfortran5:s390x. 139s Preparing to unpack .../02-libgfortran5_14.2.0-9ubuntu1_s390x.deb ... 139s Unpacking libgfortran5:s390x (14.2.0-9ubuntu1) ... 139s Selecting previously unselected package libsz2:s390x. 139s Preparing to unpack .../03-libsz2_1.1.3-1_s390x.deb ... 139s Unpacking libsz2:s390x (1.1.3-1) ... 139s Selecting previously unselected package libhdf5-103-1t64:s390x. 139s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 139s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 139s Selecting previously unselected package libhdf5-hl-100t64:s390x. 139s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 139s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 139s Selecting previously unselected package libjs-jquery. 139s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 139s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 139s Selecting previously unselected package libjs-underscore. 139s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 139s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 139s Selecting previously unselected package libjs-sphinxdoc. 139s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 139s Unpacking libjs-sphinxdoc (7.4.7-4) ... 139s Selecting previously unselected package liblapack3:s390x. 139s Preparing to unpack .../09-liblapack3_3.12.0-4_s390x.deb ... 139s Unpacking liblapack3:s390x (3.12.0-4) ... 139s Selecting previously unselected package liblbfgsb0:s390x. 139s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 139s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 139s Selecting previously unselected package liblzf1:s390x. 139s Preparing to unpack .../11-liblzf1_3.6-4_s390x.deb ... 139s Unpacking liblzf1:s390x (3.6-4) ... 139s Selecting previously unselected package python-biom-format-doc. 139s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build1_all.deb ... 139s Unpacking python-biom-format-doc (2.1.16-1build1) ... 139s Selecting previously unselected package python3-numpy. 139s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_s390x.deb ... 139s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 139s Selecting previously unselected package python3-h5py-serial. 139s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu3_s390x.deb ... 139s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 139s Selecting previously unselected package python3-h5py. 139s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu3_all.deb ... 139s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 139s Selecting previously unselected package python3-colorama. 140s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 140s Unpacking python3-colorama (0.4.6-4) ... 140s Selecting previously unselected package python3-click. 140s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 140s Unpacking python3-click (8.1.7-2) ... 140s Selecting previously unselected package python3-dateutil. 140s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 140s Unpacking python3-dateutil (2.9.0-3) ... 140s Selecting previously unselected package python3-tz. 140s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 140s Unpacking python3-tz (2024.1-2) ... 140s Selecting previously unselected package python3-pandas-lib:s390x. 140s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_s390x.deb ... 140s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 140s Selecting previously unselected package python3-pandas. 140s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 140s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 140s Selecting previously unselected package python3-decorator. 140s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 140s Unpacking python3-decorator (5.1.1-5) ... 140s Selecting previously unselected package python3-scipy. 140s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_s390x.deb ... 140s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 140s Selecting previously unselected package python3-biom-format. 140s Preparing to unpack .../24-python3-biom-format_2.1.16-1build1_s390x.deb ... 140s Unpacking python3-biom-format (2.1.16-1build1) ... 140s Setting up python3-colorama (0.4.6-4) ... 140s Setting up python3-click (8.1.7-2) ... 141s Setting up libaec0:s390x (1.1.3-1) ... 141s Setting up python3-tz (2024.1-2) ... 141s Setting up python3-decorator (5.1.1-5) ... 141s Setting up libblas3:s390x (3.12.0-4) ... 141s 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 141s Setting up liblzf1:s390x (3.6-4) ... 141s Setting up libgfortran5:s390x (14.2.0-9ubuntu1) ... 141s Setting up python3-dateutil (2.9.0-3) ... 141s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 141s Setting up libsz2:s390x (1.1.3-1) ... 141s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 141s Setting up liblapack3:s390x (3.12.0-4) ... 141s 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 141s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 143s Setting up libjs-sphinxdoc (7.4.7-4) ... 143s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 143s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 143s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 143s Setting up python3-scipy (1.13.1-5ubuntu1) ... 146s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 146s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 146s Setting up python-biom-format-doc (2.1.16-1build1) ... 146s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 151s Setting up python3-h5py (3.11.0-8ubuntu3) ... 151s Setting up python3-biom-format (2.1.16-1build1) ... 151s Processing triggers for man-db (2.13.0-1) ... 151s Processing triggers for libc-bin (2.40-1ubuntu3) ... 153s autopkgtest [14:40:12]: test run-unit-test: [----------------------- 153s 153s System information 153s ================== 153s Platform: linux 153s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 153s Python executable: /usr/bin/python3 153s 153s Dependency versions 153s =================== 153s click version: 8.1.7 153s NumPy version: 1.26.4 153s SciPy version: 1.13.1 153s h5py version: 3.11.0 153s 153s biom-format package information 153s =============================== 153s biom-format version: 2.1.16 153s 154s 154s The input file is a valid BIOM-formatted file. 154s 154s The input file is a valid BIOM-formatted file. 155s 155s The input file is a valid BIOM-formatted file. 155s 155s The input file is a valid BIOM-formatted file. 156s + table=examples/min_sparse_otu_table_hdf5.biom 156s + obsmd=examples/obs_md.txt 156s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 156s + biom show-install-info 157s 157s System information 157s ================== 157s Platform: linux 157s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 157s Python executable: /usr/bin/python3 157s 157s Dependency versions 157s =================== 157s click version: 8.1.7 157s NumPy version: 1.26.4 157s SciPy version: 1.13.1 157s h5py version: 3.11.0 157s 157s biom-format package information 157s =============================== 157s biom-format version: 2.1.16 157s 157s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 157s 158s The input file is a valid BIOM-formatted file. 158s + 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 158s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 159s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 159s + biom validate-table -i test_json.biom 160s 160s The input file is a valid BIOM-formatted file. 160s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 160s + biom validate-table -i test_hdf5.biom 161s 161s The input file is a valid BIOM-formatted file. 161s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 161s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 162s + biom validate-table -i test_hdf5.biom 162s 162s The input file is a valid BIOM-formatted file. 162s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 163s + biom validate-table -i test_json.biom 163s 163s The input file is a valid BIOM-formatted file. 163s + biom head -i examples/min_sparse_otu_table_hdf5.biom 164s # Constructed from biom file 164s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 164s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 164s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 164s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 164s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 164s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 164s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 164s Sample1 164s Sample2 164s Sample3 164s Sample4 164s Sample5 164s Sample6 164s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 165s + cat 165s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 166s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 166s Num samples: 6 166s Num observations: 5 166s Total count: 27 166s Table density (fraction of non-zero values): 0.500 166s 166s Counts/sample summary: 166s Min: 3.000 166s Max: 7.000 166s Median: 4.000 166s Mean: 4.500 166s Std. dev.: 1.500 166s Sample Metadata Categories: None provided 166s Observation Metadata Categories: None provided 166s 166s Counts/sample detail: 166s Sample2: 3.000 166s Sample5: 3.000 166s Sample3: 4.000 166s Sample6: 4.000 166s Sample4: 6.000 166s Sample1: 7.000 166s + cat 166s + biom from-uc -i uctest -o test_uc.biom 166s If this message was shown, then all commands executed without failure 166s + echo If this message was shown, then all commands executed without failure 167s autopkgtest [14:40:26]: test run-unit-test: -----------------------] 167s autopkgtest [14:40:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 167s run-unit-test PASS 168s autopkgtest [14:40:27]: test autodep8-python3: preparing testbed 274s autopkgtest [14:42:13]: testbed dpkg architecture: s390x 275s autopkgtest [14:42:14]: testbed apt version: 2.9.16 275s autopkgtest [14:42:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 275s autopkgtest [14:42:14]: testbed release detected to be: plucky 276s autopkgtest [14:42:15]: updating testbed package index (apt update) 276s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 276s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 276s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 276s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 276s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [58.3 kB] 276s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [745 kB] 277s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.2 kB] 277s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 277s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [106 kB] 277s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted s390x Packages [928 B] 277s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [578 kB] 277s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [7444 B] 277s Fetched 1593 kB in 1s (1820 kB/s) 277s Reading package lists... 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 278s Calculating upgrade... 278s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 278s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 278s autopkgtest [14:42:17]: upgrading testbed (apt dist-upgrade and autopurge) 279s Reading package lists... 279s Building dependency tree... 279s Reading state information... 279s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 279s Starting 2 pkgProblemResolver with broken count: 0 279s Done 279s Entering ResolveByKeep 279s 279s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 279s Reading package lists... 280s Building dependency tree... 280s Reading state information... 280s Starting pkgProblemResolver with broken count: 0 280s Starting 2 pkgProblemResolver with broken count: 0 280s Done 280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 282s Reading package lists... 282s Building dependency tree... 282s Reading state information... 283s Starting pkgProblemResolver with broken count: 0 283s Starting 2 pkgProblemResolver with broken count: 0 283s Done 283s The following NEW packages will be installed: 283s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 283s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 283s python3-colorama python3-dateutil python3-decorator python3-h5py 283s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 283s python3-scipy python3-tz 283s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 283s Need to get 43.9 MB of archives. 283s After this operation, 234 MB of additional disk space will be used. 283s Get:1 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 283s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-4 [238 kB] 283s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-9ubuntu1 [587 kB] 283s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 283s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 283s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 283s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-4 [2964 kB] 283s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 283s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 284s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.12.6-0ubuntu1 [890 B] 284s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 284s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py-serial s390x 3.11.0-8ubuntu3 [1655 kB] 284s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py all 3.11.0-8ubuntu3 [7982 B] 284s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 284s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB] 284s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 284s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 284s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5ubuntu1 [8010 kB] 284s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 284s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 284s Get:21 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5ubuntu1 [20.7 MB] 285s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1build1 [178 kB] 285s Fetched 43.9 MB in 2s (18.0 MB/s) 285s Selecting previously unselected package libaec0:s390x. 286s (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 ... 55869 files and directories currently installed.) 286s Preparing to unpack .../00-libaec0_1.1.3-1_s390x.deb ... 286s Unpacking libaec0:s390x (1.1.3-1) ... 286s Selecting previously unselected package libblas3:s390x. 286s Preparing to unpack .../01-libblas3_3.12.0-4_s390x.deb ... 286s Unpacking libblas3:s390x (3.12.0-4) ... 286s Selecting previously unselected package libgfortran5:s390x. 286s Preparing to unpack .../02-libgfortran5_14.2.0-9ubuntu1_s390x.deb ... 286s Unpacking libgfortran5:s390x (14.2.0-9ubuntu1) ... 286s Selecting previously unselected package libsz2:s390x. 286s Preparing to unpack .../03-libsz2_1.1.3-1_s390x.deb ... 286s Unpacking libsz2:s390x (1.1.3-1) ... 286s Selecting previously unselected package libhdf5-103-1t64:s390x. 286s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 286s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 286s Selecting previously unselected package libhdf5-hl-100t64:s390x. 286s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 286s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 286s Selecting previously unselected package liblapack3:s390x. 286s Preparing to unpack .../06-liblapack3_3.12.0-4_s390x.deb ... 286s Unpacking liblapack3:s390x (3.12.0-4) ... 286s Selecting previously unselected package liblbfgsb0:s390x. 286s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 286s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 286s Selecting previously unselected package liblzf1:s390x. 286s Preparing to unpack .../08-liblzf1_3.6-4_s390x.deb ... 286s Unpacking liblzf1:s390x (3.6-4) ... 286s Selecting previously unselected package python3-all. 286s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_s390x.deb ... 286s Unpacking python3-all (3.12.6-0ubuntu1) ... 286s Selecting previously unselected package python3-numpy. 286s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_s390x.deb ... 286s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 286s Selecting previously unselected package python3-h5py-serial. 286s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu3_s390x.deb ... 286s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 286s Selecting previously unselected package python3-h5py. 286s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu3_all.deb ... 286s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 286s Selecting previously unselected package python3-colorama. 286s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 286s Unpacking python3-colorama (0.4.6-4) ... 286s Selecting previously unselected package python3-click. 286s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 286s Unpacking python3-click (8.1.7-2) ... 286s Selecting previously unselected package python3-dateutil. 286s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 286s Unpacking python3-dateutil (2.9.0-3) ... 286s Selecting previously unselected package python3-tz. 286s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 286s Unpacking python3-tz (2024.1-2) ... 286s Selecting previously unselected package python3-pandas-lib:s390x. 286s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_s390x.deb ... 286s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 286s Selecting previously unselected package python3-pandas. 286s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 286s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 286s Selecting previously unselected package python3-decorator. 286s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 286s Unpacking python3-decorator (5.1.1-5) ... 286s Selecting previously unselected package python3-scipy. 286s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_s390x.deb ... 286s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 287s Selecting previously unselected package python3-biom-format. 287s Preparing to unpack .../21-python3-biom-format_2.1.16-1build1_s390x.deb ... 287s Unpacking python3-biom-format (2.1.16-1build1) ... 287s Setting up python3-colorama (0.4.6-4) ... 287s Setting up python3-all (3.12.6-0ubuntu1) ... 287s Setting up python3-click (8.1.7-2) ... 287s Setting up libaec0:s390x (1.1.3-1) ... 287s Setting up python3-tz (2024.1-2) ... 287s Setting up python3-decorator (5.1.1-5) ... 287s Setting up libblas3:s390x (3.12.0-4) ... 287s 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 287s Setting up liblzf1:s390x (3.6-4) ... 287s Setting up libgfortran5:s390x (14.2.0-9ubuntu1) ... 287s Setting up python3-dateutil (2.9.0-3) ... 287s Setting up libsz2:s390x (1.1.3-1) ... 287s Setting up liblapack3:s390x (3.12.0-4) ... 287s 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 287s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 289s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 289s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 289s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 289s Setting up python3-scipy (1.13.1-5ubuntu1) ... 292s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 292s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 293s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 298s Setting up python3-h5py (3.11.0-8ubuntu3) ... 298s Setting up python3-biom-format (2.1.16-1build1) ... 298s Processing triggers for man-db (2.13.0-1) ... 298s Processing triggers for libc-bin (2.40-1ubuntu3) ... 302s autopkgtest [14:42:41]: 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 302s autopkgtest [14:42:41]: test autodep8-python3: [----------------------- 302s Testing with python3.12: 303s 303s autopkgtest [14:42:42]: test autodep8-python3: -----------------------] 304s autopkgtest [14:42:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 304s autodep8-python3 PASS (superficial) 304s autopkgtest [14:42:43]: @@@@@@@@@@@@@@@@@@@@ summary 304s run-unit-test PASS 304s autodep8-python3 PASS (superficial) 316s nova [W] Using flock in prodstack6-s390x 316s flock: timeout while waiting to get lock 316s Creating nova instance adt-plucky-s390x-python-biom-format-20241204-143739-juju-7f2275-prod-proposed-migration-environment-20-19d430af-d9bc-4a4b-a911-7bb392784037 from image adt/ubuntu-plucky-s390x-server-20241204.img (UUID 89b4900b-e439-4dd9-be41-eb47bd412513)... 316s nova [W] Using flock in prodstack6-s390x 316s Creating nova instance adt-plucky-s390x-python-biom-format-20241204-143739-juju-7f2275-prod-proposed-migration-environment-20-19d430af-d9bc-4a4b-a911-7bb392784037 from image adt/ubuntu-plucky-s390x-server-20241204.img (UUID 89b4900b-e439-4dd9-be41-eb47bd412513)...