0s autopkgtest [16:33:45]: starting date and time: 2024-11-18 16:33:45+0000 0s autopkgtest [16:33:45]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:33:45]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.dkkdedyb/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:openmpi,src:sphinx-rtd-theme --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu1 openmpi/5.0.5-6 sphinx-rtd-theme/3.0.2+dfsg-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-s390x-20.secgroup --name adt-plucky-s390x-python-biom-format-20241118-163345-juju-7f2275-prod-proposed-migration-environment-20-0220e5d8-4732-485f-8205-62de008951c4 --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/ 112s autopkgtest [16:35:37]: testbed dpkg architecture: s390x 112s autopkgtest [16:35:37]: testbed apt version: 2.9.8 112s autopkgtest [16:35:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 113s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 113s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 114s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [85.5 kB] 114s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [585 kB] 114s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3760 B] 114s Fetched 1655 kB in 1s (1505 kB/s) 114s Reading package lists... 116s Reading package lists... 116s Building dependency tree... 116s Reading state information... 117s Calculating upgrade... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 117s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 117s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 118s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 118s Reading package lists... 118s Reading package lists... 118s Building dependency tree... 118s Reading state information... 118s Calculating upgrade... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s Reading package lists... 119s Building dependency tree... 119s Reading state information... 119s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s autopkgtest [16:35:46]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 121s autopkgtest [16:35:46]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 124s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B] 124s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB] 124s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB] 125s gpgv: Signature made Mon May 27 20:43:46 2024 UTC 125s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 125s gpgv: issuer "emollier@debian.org" 125s gpgv: Can't check signature: No public key 125s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found 125s autopkgtest [16:35:50]: testing package python-biom-format version 2.1.16-1 125s autopkgtest [16:35:50]: build not needed 127s autopkgtest [16:35:52]: test run-unit-test: preparing testbed 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Starting pkgProblemResolver with broken count: 0 134s Starting 2 pkgProblemResolver with broken count: 0 134s Done 135s The following additional packages will be installed: 135s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 135s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 135s libsz2 python-biom-format-doc python3-biom-format python3-click 135s python3-colorama python3-dateutil python3-decorator python3-h5py 135s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 135s python3-scipy python3-tz 135s Suggested packages: 135s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 135s python-pandas-doc python3-statsmodels python-scipy-doc 135s Recommended packages: 135s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 135s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 135s python3-tables g++ | c++-compiler python3-pil 135s The following NEW packages will be installed: 135s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 135s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 135s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 135s python3-click python3-colorama python3-dateutil python3-decorator 135s python3-h5py python3-h5py-serial python3-numpy python3-pandas 135s python3-pandas-lib python3-scipy python3-tz 135s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 135s Need to get 44.5 MB/44.5 MB of archives. 135s After this operation, 235 MB of additional disk space will be used. 135s Get:1 /tmp/autopkgtest.ebZxUc/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B] 135s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 135s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 135s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 135s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 135s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 135s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 135s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 135s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 135s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB] 135s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 135s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 135s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 135s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biom-format-doc all 2.1.16-1 [57.5 kB] 135s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 135s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py-serial s390x 3.11.0-8ubuntu1 [1654 kB] 136s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py all 3.11.0-8ubuntu1 [7982 B] 136s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 136s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB] 136s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 136s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 136s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5ubuntu1 [8010 kB] 136s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 137s Get:24 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 137s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5ubuntu1 [20.7 MB] 138s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1 [147 kB] 139s Fetched 44.5 MB in 5s (9614 kB/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 ... 55538 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_3.12.0-3build2_s390x.deb ... 139s Unpacking libblas3:s390x (3.12.0-3build2) ... 139s Selecting previously unselected package libgfortran5:s390x. 139s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 139s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 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_3.12.0-3build2_s390x.deb ... 139s Unpacking liblapack3:s390x (3.12.0-3build2) ... 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_2.1.16-1_all.deb ... 139s Unpacking python-biom-format-doc (2.1.16-1) ... 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_3.11.0-8ubuntu1_s390x.deb ... 139s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 139s Selecting previously unselected package python3-h5py. 139s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu1_all.deb ... 139s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 139s Selecting previously unselected package python3-colorama. 139s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 139s Unpacking python3-colorama (0.4.6-4) ... 139s Selecting previously unselected package python3-click. 139s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 139s Unpacking python3-click (8.1.7-2) ... 139s Selecting previously unselected package python3-dateutil. 139s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 139s Unpacking python3-dateutil (2.9.0-3) ... 139s Selecting previously unselected package python3-tz. 139s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 139s Unpacking python3-tz (2024.1-2) ... 139s Selecting previously unselected package python3-pandas-lib:s390x. 139s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_s390x.deb ... 139s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 139s Selecting previously unselected package python3-pandas. 139s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 139s 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_2.1.16-1_s390x.deb ... 140s Unpacking python3-biom-format (2.1.16-1) ... 140s Selecting previously unselected package autopkgtest-satdep. 140s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 140s Unpacking autopkgtest-satdep (0) ... 140s Setting up python3-colorama (0.4.6-4) ... 140s Setting up python3-click (8.1.7-2) ... 140s Setting up libaec0:s390x (1.1.3-1) ... 140s Setting up python3-tz (2024.1-2) ... 140s Setting up python3-decorator (5.1.1-5) ... 140s Setting up libblas3:s390x (3.12.0-3build2) ... 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 (14.2.0-8ubuntu1) ... 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 (3.12.0-3build2) ... 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 (3.11.0-8ubuntu1) ... 146s Setting up python-biom-format-doc (2.1.16-1) ... 146s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 151s Setting up python3-h5py (3.11.0-8ubuntu1) ... 151s Setting up python3-biom-format (2.1.16-1) ... 151s Setting up autopkgtest-satdep (0) ... 151s Processing triggers for man-db (2.13.0-1) ... 152s Processing triggers for libc-bin (2.40-1ubuntu3) ... 154s (Reading database ... 60249 files and directories currently installed.) 154s Removing autopkgtest-satdep (0) ... 154s autopkgtest [16:36:19]: test run-unit-test: [----------------------- 155s 155s System information 155s ================== 155s Platform: linux 155s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 155s Python executable: /usr/bin/python3 155s 155s Dependency versions 155s =================== 155s click version: 8.1.7 155s NumPy version: 1.26.4 155s SciPy version: 1.13.1 155s h5py version: 3.11.0 155s 155s biom-format package information 155s =============================== 155s biom-format version: 2.1.16 155s 156s 156s The input file is a valid BIOM-formatted file. 156s 156s The input file is a valid BIOM-formatted file. 157s 157s The input file is a valid BIOM-formatted file. 157s 157s The input file is a valid BIOM-formatted file. 158s + table=examples/min_sparse_otu_table_hdf5.biom 158s + obsmd=examples/obs_md.txt 158s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 158s + biom show-install-info 159s 159s System information 159s ================== 159s Platform: linux 159s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 159s Python executable: /usr/bin/python3 159s 159s Dependency versions 159s =================== 159s click version: 8.1.7 159s NumPy version: 1.26.4 159s SciPy version: 1.13.1 159s h5py version: 3.11.0 159s 159s biom-format package information 159s =============================== 159s biom-format version: 2.1.16 159s 159s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 159s 159s The input file is a valid BIOM-formatted file. 159s + 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 160s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 161s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 161s + biom validate-table -i test_json.biom 162s 162s The input file is a valid BIOM-formatted file. 162s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 162s + biom validate-table -i test_hdf5.biom 163s 163s The input file is a valid BIOM-formatted file. 163s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 163s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 164s + biom validate-table -i test_hdf5.biom 164s 164s The input file is a valid BIOM-formatted file. 164s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 165s + biom validate-table -i test_json.biom 165s 165s The input file is a valid BIOM-formatted file. 166s + biom head -i examples/min_sparse_otu_table_hdf5.biom 166s # Constructed from biom file 166s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 166s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 166s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 166s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 166s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 166s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 166s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 167s Sample1 167s Sample2 167s Sample3 167s Sample4 167s Sample5 167s Sample6 167s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 167s + cat 167s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 168s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 168s Num samples: 6 168s Num observations: 5 168s Total count: 27 168s Table density (fraction of non-zero values): 0.500 168s 168s Counts/sample summary: 168s Min: 3.000 168s Max: 7.000 168s Median: 4.000 168s Mean: 4.500 168s Std. dev.: 1.500 168s Sample Metadata Categories: None provided 168s Observation Metadata Categories: None provided 168s 168s Counts/sample detail: 168s Sample2: 3.000 168s Sample5: 3.000 168s Sample3: 4.000 168s Sample6: 4.000 168s Sample4: 6.000 168s Sample1: 7.000 168s + cat 168s + biom from-uc -i uctest -o test_uc.biom 169s If this message was shown, then all commands executed without failure 169s + echo If this message was shown, then all commands executed without failure 169s autopkgtest [16:36:34]: test run-unit-test: -----------------------] 170s run-unit-test PASS 170s autopkgtest [16:36:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 170s autopkgtest [16:36:35]: test autodep8-python3: preparing testbed 250s autopkgtest [16:37:55]: testbed dpkg architecture: s390x 250s autopkgtest [16:37:55]: testbed apt version: 2.9.8 250s autopkgtest [16:37:55]: @@@@@@@@@@@@@@@@@@@@ test bed setup 251s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 251s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 252s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 252s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 252s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 252s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [85.5 kB] 252s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [585 kB] 252s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [3760 B] 252s Fetched 1655 kB in 1s (2186 kB/s) 252s Reading package lists... 254s Reading package lists... 254s Building dependency tree... 254s Reading state information... 254s Calculating upgrade... 254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 254s Reading package lists... 254s Building dependency tree... 254s Reading state information... 254s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 254s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 255s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 255s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 255s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 255s Reading package lists... 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 256s Calculating upgrade... 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 256s Reading package lists... 256s Building dependency tree... 256s Reading state information... 256s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 261s Reading package lists... 261s Building dependency tree... 261s Reading state information... 261s Starting pkgProblemResolver with broken count: 0 261s Starting 2 pkgProblemResolver with broken count: 0 261s Done 261s The following additional packages will be installed: 261s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 261s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 261s python3-colorama python3-dateutil python3-decorator python3-h5py 261s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 261s python3-scipy python3-tz 261s Suggested packages: 261s python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc 261s python3-dev python3-pytest python-pandas-doc python3-statsmodels 261s python-scipy-doc 261s Recommended packages: 261s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 261s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 261s g++ | c++-compiler python3-pil 261s The following NEW packages will be installed: 261s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 261s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all 261s python3-biom-format python3-click python3-colorama python3-dateutil 261s python3-decorator python3-h5py python3-h5py-serial python3-numpy 261s python3-pandas python3-pandas-lib python3-scipy python3-tz 261s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 261s Need to get 43.8 MB/43.8 MB of archives. 261s After this operation, 234 MB of additional disk space will be used. 261s Get:1 /tmp/autopkgtest.ebZxUc/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 261s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB] 261s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 261s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 262s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B] 262s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB] 262s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB] 262s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 262s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 262s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B] 262s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x python3-all s390x 3.12.6-0ubuntu1 [890 B] 262s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11ubuntu1 [4602 kB] 262s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py-serial s390x 3.11.0-8ubuntu1 [1654 kB] 262s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x python3-h5py all 3.11.0-8ubuntu1 [7982 B] 262s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB] 262s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB] 262s Get:17 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-3 [80.2 kB] 262s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB] 262s Get:19 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5ubuntu1 [8010 kB] 262s Get:20 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 262s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 262s Get:22 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5ubuntu1 [20.7 MB] 263s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1 [147 kB] 263s Fetched 43.8 MB in 2s (22.5 MB/s) 263s Selecting previously unselected package libaec0:s390x. 263s (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 ... 55538 files and directories currently installed.) 263s Preparing to unpack .../00-libaec0_1.1.3-1_s390x.deb ... 263s Unpacking libaec0:s390x (1.1.3-1) ... 263s Selecting previously unselected package libblas3:s390x. 263s Preparing to unpack .../01-libblas3_3.12.0-3build2_s390x.deb ... 263s Unpacking libblas3:s390x (3.12.0-3build2) ... 263s Selecting previously unselected package libgfortran5:s390x. 263s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 263s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 263s Selecting previously unselected package libsz2:s390x. 263s Preparing to unpack .../03-libsz2_1.1.3-1_s390x.deb ... 263s Unpacking libsz2:s390x (1.1.3-1) ... 263s Selecting previously unselected package libhdf5-103-1t64:s390x. 263s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ... 263s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 263s Selecting previously unselected package libhdf5-hl-100t64:s390x. 263s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ... 263s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 263s Selecting previously unselected package liblapack3:s390x. 263s Preparing to unpack .../06-liblapack3_3.12.0-3build2_s390x.deb ... 263s Unpacking liblapack3:s390x (3.12.0-3build2) ... 263s Selecting previously unselected package liblbfgsb0:s390x. 263s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 263s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 263s Selecting previously unselected package liblzf1:s390x. 263s Preparing to unpack .../08-liblzf1_3.6-4_s390x.deb ... 263s Unpacking liblzf1:s390x (3.6-4) ... 263s Selecting previously unselected package python3-all. 263s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_s390x.deb ... 263s Unpacking python3-all (3.12.6-0ubuntu1) ... 263s Selecting previously unselected package python3-numpy. 263s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_s390x.deb ... 263s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 264s Selecting previously unselected package python3-h5py-serial. 264s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu1_s390x.deb ... 264s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 264s Selecting previously unselected package python3-h5py. 264s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu1_all.deb ... 264s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 264s Selecting previously unselected package python3-colorama. 264s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 264s Unpacking python3-colorama (0.4.6-4) ... 264s Selecting previously unselected package python3-click. 264s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 264s Unpacking python3-click (8.1.7-2) ... 264s Selecting previously unselected package python3-dateutil. 264s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 264s Unpacking python3-dateutil (2.9.0-3) ... 264s Selecting previously unselected package python3-tz. 264s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 264s Unpacking python3-tz (2024.1-2) ... 264s Selecting previously unselected package python3-pandas-lib:s390x. 264s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_s390x.deb ... 264s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 264s Selecting previously unselected package python3-pandas. 264s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 264s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 264s Selecting previously unselected package python3-decorator. 264s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 264s Unpacking python3-decorator (5.1.1-5) ... 264s Selecting previously unselected package python3-scipy. 264s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_s390x.deb ... 264s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 264s Selecting previously unselected package python3-biom-format. 264s Preparing to unpack .../21-python3-biom-format_2.1.16-1_s390x.deb ... 264s Unpacking python3-biom-format (2.1.16-1) ... 264s Selecting previously unselected package autopkgtest-satdep. 264s Preparing to unpack .../22-2-autopkgtest-satdep.deb ... 264s Unpacking autopkgtest-satdep (0) ... 264s Setting up python3-colorama (0.4.6-4) ... 265s Setting up python3-all (3.12.6-0ubuntu1) ... 265s Setting up python3-click (8.1.7-2) ... 265s Setting up libaec0:s390x (1.1.3-1) ... 265s Setting up python3-tz (2024.1-2) ... 265s Setting up python3-decorator (5.1.1-5) ... 265s Setting up libblas3:s390x (3.12.0-3build2) ... 265s 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 265s Setting up liblzf1:s390x (3.6-4) ... 265s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 265s Setting up python3-dateutil (2.9.0-3) ... 265s Setting up libsz2:s390x (1.1.3-1) ... 265s Setting up liblapack3:s390x (3.12.0-3build2) ... 265s 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 265s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 267s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ... 267s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 267s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ... 267s Setting up python3-scipy (1.13.1-5ubuntu1) ... 270s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-5ubuntu1) ... 270s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 270s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 275s Setting up python3-h5py (3.11.0-8ubuntu1) ... 275s Setting up python3-biom-format (2.1.16-1) ... 275s Setting up autopkgtest-satdep (0) ... 275s Processing triggers for man-db (2.13.0-1) ... 275s Processing triggers for libc-bin (2.40-1ubuntu3) ... 277s (Reading database ... 60151 files and directories currently installed.) 277s Removing autopkgtest-satdep (0) ... 282s autopkgtest [16:38:27]: 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 282s autopkgtest [16:38:27]: test autodep8-python3: [----------------------- 282s Testing with python3.12: 283s 283s autopkgtest [16:38:28]: test autodep8-python3: -----------------------] 284s autodep8-python3 PASS (superficial) 284s autopkgtest [16:38:29]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 284s autopkgtest [16:38:29]: @@@@@@@@@@@@@@@@@@@@ summary 284s run-unit-test PASS 284s autodep8-python3 PASS (superficial) 295s nova [W] Using flock in prodstack6-s390x 295s flock: timeout while waiting to get lock 295s Creating nova instance adt-plucky-s390x-python-biom-format-20241118-163345-juju-7f2275-prod-proposed-migration-environment-20-0220e5d8-4732-485f-8205-62de008951c4 from image adt/ubuntu-plucky-s390x-server-20241118.img (UUID 7dde37bf-57a6-4020-8415-6d0f6608b9a5)... 295s nova [W] Using flock in prodstack6-s390x 295s Creating nova instance adt-plucky-s390x-python-biom-format-20241118-163345-juju-7f2275-prod-proposed-migration-environment-20-0220e5d8-4732-485f-8205-62de008951c4 from image adt/ubuntu-plucky-s390x-server-20241118.img (UUID 7dde37bf-57a6-4020-8415-6d0f6608b9a5)...