0s autopkgtest [18:57:15]: starting date and time: 2024-11-18 18:57:15+0000 0s autopkgtest [18:57:15]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [18:57:15]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.29ne33u0/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@lcy02-9.secgroup --name adt-plucky-amd64-python-biom-format-20241118-185715-juju-7f2275-prod-proposed-migration-environment-15-7f776e5f-6d42-43af-9bcd-b55c96e0a935 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 51s autopkgtest [18:58:06]: testbed dpkg architecture: amd64 51s autopkgtest [18:58:06]: testbed apt version: 2.9.8 51s autopkgtest [18:58:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 51s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 51s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 51s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.2 kB] 51s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 51s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [815 kB] 51s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [64.6 kB] 51s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 51s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 51s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [258 kB] 51s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [659 kB] 51s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [772 B] 51s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [7272 B] 51s Fetched 2115 kB in 0s (7573 kB/s) 51s Reading package lists... 53s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Calculating upgrade... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 53s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 54s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 54s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 54s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 54s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 55s Reading package lists... 55s Reading package lists... 56s Building dependency tree... 56s Reading state information... 56s Calculating upgrade... 56s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 56s Reading package lists... 56s Building dependency tree... 56s Reading state information... 57s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 57s autopkgtest [18:58:12]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 57s autopkgtest [18:58:12]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 59s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B] 59s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB] 59s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB] 59s gpgv: Signature made Mon May 27 20:43:46 2024 UTC 59s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 59s gpgv: issuer "emollier@debian.org" 59s gpgv: Can't check signature: No public key 59s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found 59s autopkgtest [18:58:14]: testing package python-biom-format version 2.1.16-1 59s autopkgtest [18:58:14]: build not needed 60s autopkgtest [18:58:15]: test run-unit-test: preparing testbed 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 62s The following additional packages will be installed: 62s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 62s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 62s libsz2 python-biom-format-doc python3-biom-format python3-click 62s python3-colorama python3-dateutil python3-decorator python3-h5py 62s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 62s python3-scipy python3-tz 62s Suggested packages: 62s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 62s python-pandas-doc python3-statsmodels python-scipy-doc 62s Recommended packages: 62s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 62s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 62s python3-tables python3-numba g++ | c++-compiler python3-pil 62s The following NEW packages will be installed: 62s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 62s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 62s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 62s python3-click python3-colorama python3-dateutil python3-decorator 62s python3-h5py python3-h5py-serial python3-numpy python3-pandas 62s python3-pandas-lib python3-scipy python3-tz 62s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 62s Need to get 46.3 MB/46.3 MB of archives. 62s After this operation, 258 MB of additional disk space will be used. 62s Get:1 /tmp/autopkgtest.Cv7ks0/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B] 62s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 62s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 62s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 62s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 62s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 62s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 62s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 62s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 62s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 62s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 62s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 62s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 62s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biom-format-doc all 2.1.16-1 [57.5 kB] 62s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 62s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu1 [1686 kB] 62s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py all 3.11.0-8ubuntu1 [7982 B] 62s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 62s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 62s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 62s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 62s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 62s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 62s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 62s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 62s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB] 62s Fetched 46.3 MB in 0s (117 MB/s) 63s Selecting previously unselected package libaec0:amd64. 63s (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 ... 75620 files and directories currently installed.) 63s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 63s Unpacking libaec0:amd64 (1.1.3-1) ... 63s Selecting previously unselected package libblas3:amd64. 63s Preparing to unpack .../01-libblas3_3.12.0-3build2_amd64.deb ... 63s Unpacking libblas3:amd64 (3.12.0-3build2) ... 63s Selecting previously unselected package libgfortran5:amd64. 63s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 63s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 63s Selecting previously unselected package libsz2:amd64. 63s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ... 63s Unpacking libsz2:amd64 (1.1.3-1) ... 63s Selecting previously unselected package libhdf5-103-1t64:amd64. 63s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 63s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 63s Selecting previously unselected package libhdf5-hl-100t64:amd64. 63s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 63s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 63s Selecting previously unselected package libjs-jquery. 63s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 63s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 63s Selecting previously unselected package libjs-underscore. 63s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 63s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 63s Selecting previously unselected package libjs-sphinxdoc. 63s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 63s Unpacking libjs-sphinxdoc (7.4.7-4) ... 63s Selecting previously unselected package liblapack3:amd64. 63s Preparing to unpack .../09-liblapack3_3.12.0-3build2_amd64.deb ... 63s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 63s Selecting previously unselected package liblbfgsb0:amd64. 63s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 63s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 63s Selecting previously unselected package liblzf1:amd64. 63s Preparing to unpack .../11-liblzf1_3.6-4_amd64.deb ... 63s Unpacking liblzf1:amd64 (3.6-4) ... 63s Selecting previously unselected package python-biom-format-doc. 63s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ... 63s Unpacking python-biom-format-doc (2.1.16-1) ... 63s Selecting previously unselected package python3-numpy. 63s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 63s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 64s Selecting previously unselected package python3-h5py-serial. 64s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu1_amd64.deb ... 64s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 64s Selecting previously unselected package python3-h5py. 64s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu1_all.deb ... 64s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 64s Selecting previously unselected package python3-colorama. 64s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 64s Unpacking python3-colorama (0.4.6-4) ... 64s Selecting previously unselected package python3-click. 64s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 64s Unpacking python3-click (8.1.7-2) ... 64s Selecting previously unselected package python3-dateutil. 64s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 64s Unpacking python3-dateutil (2.9.0-3) ... 64s Selecting previously unselected package python3-tz. 64s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 64s Unpacking python3-tz (2024.1-2) ... 64s Selecting previously unselected package python3-pandas-lib:amd64. 64s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_amd64.deb ... 64s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 64s Selecting previously unselected package python3-pandas. 64s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 64s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 64s Selecting previously unselected package python3-decorator. 64s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 64s Unpacking python3-decorator (5.1.1-5) ... 64s Selecting previously unselected package python3-scipy. 64s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 64s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 65s Selecting previously unselected package python3-biom-format. 65s Preparing to unpack .../24-python3-biom-format_2.1.16-1_amd64.deb ... 65s Unpacking python3-biom-format (2.1.16-1) ... 65s Selecting previously unselected package autopkgtest-satdep. 65s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 65s Unpacking autopkgtest-satdep (0) ... 65s Setting up python3-colorama (0.4.6-4) ... 65s Setting up python3-click (8.1.7-2) ... 65s Setting up libaec0:amd64 (1.1.3-1) ... 65s Setting up python3-tz (2024.1-2) ... 66s Setting up python3-decorator (5.1.1-5) ... 66s Setting up libblas3:amd64 (3.12.0-3build2) ... 66s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 66s Setting up liblzf1:amd64 (3.6-4) ... 66s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 66s Setting up python3-dateutil (2.9.0-3) ... 66s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 66s Setting up libsz2:amd64 (1.1.3-1) ... 66s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 66s Setting up liblapack3:amd64 (3.12.0-3build2) ... 66s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 66s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 68s Setting up libjs-sphinxdoc (7.4.7-4) ... 68s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 68s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 68s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 68s Setting up python3-scipy (1.13.1-5ubuntu1) ... 71s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 71s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 71s Setting up python-biom-format-doc (2.1.16-1) ... 71s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 75s Setting up python3-h5py (3.11.0-8ubuntu1) ... 75s Setting up python3-biom-format (2.1.16-1) ... 76s Setting up autopkgtest-satdep (0) ... 76s Processing triggers for man-db (2.13.0-1) ... 76s Processing triggers for libc-bin (2.40-1ubuntu3) ... 78s (Reading database ... 80331 files and directories currently installed.) 78s Removing autopkgtest-satdep (0) ... 79s autopkgtest [18:58:34]: test run-unit-test: [----------------------- 80s 80s System information 80s ================== 80s Platform: linux 80s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 80s Python executable: /usr/bin/python3 80s 80s Dependency versions 80s =================== 80s click version: 8.1.7 80s NumPy version: 1.26.4 80s SciPy version: 1.13.1 80s h5py version: 3.11.0 80s 80s biom-format package information 80s =============================== 80s biom-format version: 2.1.16 80s 80s 80s The input file is a valid BIOM-formatted file. 81s 81s The input file is a valid BIOM-formatted file. 82s 82s The input file is a valid BIOM-formatted file. 82s 82s The input file is a valid BIOM-formatted file. 84s + table=examples/min_sparse_otu_table_hdf5.biom 84s + obsmd=examples/obs_md.txt 84s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 84s + biom show-install-info 85s 85s System information 85s ================== 85s Platform: linux 85s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 85s Python executable: /usr/bin/python3 85s 85s Dependency versions 85s =================== 85s click version: 8.1.7 85s NumPy version: 1.26.4 85s SciPy version: 1.13.1 85s h5py version: 3.11.0 85s 85s biom-format package information 85s =============================== 85s biom-format version: 2.1.16 85s 85s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 85s 85s The input file is a valid BIOM-formatted file. 86s + 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 86s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 87s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 88s + biom validate-table -i test_json.biom 88s 88s The input file is a valid BIOM-formatted file. 89s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 89s + biom validate-table -i test_hdf5.biom 90s 90s The input file is a valid BIOM-formatted file. 90s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 91s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 92s + biom validate-table -i test_hdf5.biom 92s 92s The input file is a valid BIOM-formatted file. 92s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 93s + biom validate-table -i test_json.biom 94s 94s The input file is a valid BIOM-formatted file. 94s + biom head -i examples/min_sparse_otu_table_hdf5.biom 94s # Constructed from biom file 94s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 94s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 94s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 94s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 94s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 94s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 95s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 95s Sample1 95s Sample2 95s Sample3 95s Sample4 95s Sample5 95s Sample6 95s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 96s + cat 96s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 97s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 98s Num samples: 6 98s Num observations: 5 98s Total count: 27 98s Table density (fraction of non-zero values): 0.500 98s 98s Counts/sample summary: 98s Min: 3.000 98s Max: 7.000 98s Median: 4.000 98s Mean: 4.500 98s Std. dev.: 1.500 98s Sample Metadata Categories: None provided 98s Observation Metadata Categories: None provided 98s 98s Counts/sample detail: 98s Sample2: 3.000 98s Sample5: 3.000 98s Sample3: 4.000 98s Sample6: 4.000 98s Sample4: 6.000 98s Sample1: 7.000 98s + cat 98s + biom from-uc -i uctest -o test_uc.biom 98s If this message was shown, then all commands executed without failure 98s + echo If this message was shown, then all commands executed without failure 99s autopkgtest [18:58:54]: test run-unit-test: -----------------------] 99s run-unit-test PASS 99s autopkgtest [18:58:54]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 99s autopkgtest [18:58:54]: test autodep8-python3: preparing testbed 154s autopkgtest [18:59:49]: testbed dpkg architecture: amd64 154s autopkgtest [18:59:49]: testbed apt version: 2.9.8 154s autopkgtest [18:59:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 155s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 155s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 155s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 155s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [815 kB] 155s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.2 kB] 155s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 155s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [64.6 kB] 155s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 155s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [258 kB] 155s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [659 kB] 155s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [7272 B] 155s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [772 B] 155s Fetched 2115 kB in 0s (5613 kB/s) 155s Reading package lists... 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s Calculating upgrade... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Reading package lists... 158s Building dependency tree... 158s Reading state information... 158s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 158s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 158s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 158s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 159s Reading package lists... 159s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s Calculating upgrade... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s Reading package lists... 161s Building dependency tree... 161s Reading state information... 161s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 162s Reading package lists... 162s Building dependency tree... 162s Reading state information... 163s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 163s The following additional packages will be installed: 163s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 163s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 163s python3-colorama python3-dateutil python3-decorator python3-h5py 163s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 163s python3-scipy python3-tz 163s Suggested packages: 163s python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc 163s python3-dev python3-pytest python-pandas-doc python3-statsmodels 163s python-scipy-doc 163s Recommended packages: 163s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 163s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 163s python3-numba g++ | c++-compiler python3-pil 163s The following NEW packages will be installed: 163s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 163s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all 163s python3-biom-format python3-click python3-colorama python3-dateutil 163s python3-decorator python3-h5py python3-h5py-serial python3-numpy 163s python3-pandas python3-pandas-lib python3-scipy python3-tz 163s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 163s Need to get 45.7 MB/45.7 MB of archives. 163s After this operation, 256 MB of additional disk space will be used. 163s Get:1 /tmp/autopkgtest.Cv7ks0/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 163s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 163s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 163s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 163s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 163s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 163s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 163s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 164s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 164s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 164s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 164s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 164s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu1 [1686 kB] 164s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py all 3.11.0-8ubuntu1 [7982 B] 164s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 164s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 164s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 164s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 164s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 164s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 164s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 164s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 164s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB] 164s Fetched 45.7 MB in 0s (111 MB/s) 164s Selecting previously unselected package libaec0:amd64. 164s (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 ... 75620 files and directories currently installed.) 164s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 164s Unpacking libaec0:amd64 (1.1.3-1) ... 164s Selecting previously unselected package libblas3:amd64. 164s Preparing to unpack .../01-libblas3_3.12.0-3build2_amd64.deb ... 164s Unpacking libblas3:amd64 (3.12.0-3build2) ... 164s Selecting previously unselected package libgfortran5:amd64. 164s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 164s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 164s Selecting previously unselected package libsz2:amd64. 164s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ... 164s Unpacking libsz2:amd64 (1.1.3-1) ... 164s Selecting previously unselected package libhdf5-103-1t64:amd64. 164s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 164s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 165s Selecting previously unselected package libhdf5-hl-100t64:amd64. 165s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 165s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 165s Selecting previously unselected package liblapack3:amd64. 165s Preparing to unpack .../06-liblapack3_3.12.0-3build2_amd64.deb ... 165s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 165s Selecting previously unselected package liblbfgsb0:amd64. 165s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 165s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 165s Selecting previously unselected package liblzf1:amd64. 165s Preparing to unpack .../08-liblzf1_3.6-4_amd64.deb ... 165s Unpacking liblzf1:amd64 (3.6-4) ... 165s Selecting previously unselected package python3-all. 165s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_amd64.deb ... 165s Unpacking python3-all (3.12.6-0ubuntu1) ... 165s Selecting previously unselected package python3-numpy. 165s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 165s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 165s Selecting previously unselected package python3-h5py-serial. 165s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu1_amd64.deb ... 165s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 165s Selecting previously unselected package python3-h5py. 165s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu1_all.deb ... 165s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 165s Selecting previously unselected package python3-colorama. 165s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 165s Unpacking python3-colorama (0.4.6-4) ... 165s Selecting previously unselected package python3-click. 165s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 165s Unpacking python3-click (8.1.7-2) ... 165s Selecting previously unselected package python3-dateutil. 165s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 165s Unpacking python3-dateutil (2.9.0-3) ... 165s Selecting previously unselected package python3-tz. 165s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 165s Unpacking python3-tz (2024.1-2) ... 165s Selecting previously unselected package python3-pandas-lib:amd64. 165s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_amd64.deb ... 165s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 166s Selecting previously unselected package python3-pandas. 166s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 166s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 166s Selecting previously unselected package python3-decorator. 166s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 166s Unpacking python3-decorator (5.1.1-5) ... 166s Selecting previously unselected package python3-scipy. 166s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 166s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 167s Selecting previously unselected package python3-biom-format. 167s Preparing to unpack .../21-python3-biom-format_2.1.16-1_amd64.deb ... 167s Unpacking python3-biom-format (2.1.16-1) ... 167s Selecting previously unselected package autopkgtest-satdep. 167s Preparing to unpack .../22-2-autopkgtest-satdep.deb ... 167s Unpacking autopkgtest-satdep (0) ... 167s Setting up python3-colorama (0.4.6-4) ... 167s Setting up python3-all (3.12.6-0ubuntu1) ... 167s Setting up python3-click (8.1.7-2) ... 167s Setting up libaec0:amd64 (1.1.3-1) ... 167s Setting up python3-tz (2024.1-2) ... 167s Setting up python3-decorator (5.1.1-5) ... 167s Setting up libblas3:amd64 (3.12.0-3build2) ... 167s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 167s Setting up liblzf1:amd64 (3.6-4) ... 167s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 167s Setting up python3-dateutil (2.9.0-3) ... 167s Setting up libsz2:amd64 (1.1.3-1) ... 167s Setting up liblapack3:amd64 (3.12.0-3build2) ... 167s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 167s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 169s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 169s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 169s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 169s Setting up python3-scipy (1.13.1-5ubuntu1) ... 172s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 172s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 173s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 177s Setting up python3-h5py (3.11.0-8ubuntu1) ... 177s Setting up python3-biom-format (2.1.16-1) ... 178s Setting up autopkgtest-satdep (0) ... 178s Processing triggers for man-db (2.13.0-1) ... 178s Processing triggers for libc-bin (2.40-1ubuntu3) ... 180s (Reading database ... 80233 files and directories currently installed.) 180s Removing autopkgtest-satdep (0) ... 181s autopkgtest [19:00:16]: 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 181s autopkgtest [19:00:16]: test autodep8-python3: [----------------------- 181s Testing with python3.12: 182s 183s autopkgtest [19:00:18]: test autodep8-python3: -----------------------] 183s autodep8-python3 PASS (superficial) 183s autopkgtest [19:00:18]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 183s autopkgtest [19:00:18]: @@@@@@@@@@@@@@@@@@@@ summary 183s run-unit-test PASS 183s autodep8-python3 PASS (superficial) 192s nova [W] Skipping flock for amd64 192s Creating nova instance adt-plucky-amd64-python-biom-format-20241118-185715-juju-7f2275-prod-proposed-migration-environment-15-7f776e5f-6d42-43af-9bcd-b55c96e0a935 from image adt/ubuntu-plucky-amd64-server-20241118.img (UUID a445057a-6704-405a-bc03-181ba96486b5)... 192s nova [W] Skipping flock for amd64 192s Creating nova instance adt-plucky-amd64-python-biom-format-20241118-185715-juju-7f2275-prod-proposed-migration-environment-15-7f776e5f-6d42-43af-9bcd-b55c96e0a935 from image adt/ubuntu-plucky-amd64-server-20241118.img (UUID a445057a-6704-405a-bc03-181ba96486b5)...