0s autopkgtest [10:57:52]: starting date and time: 2024-12-02 10:57:52+0000 0s autopkgtest [10:57:52]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [10:57:52]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kjbmh_re/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/5.0.6-2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-30.secgroup --name adt-plucky-amd64-python-biom-format-20241202-105752-juju-7f2275-prod-proposed-migration-environment-15-2cf4d68a-839d-4d5e-aa0c-696f3aac6965 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 651s autopkgtest [11:08:43]: testbed dpkg architecture: amd64 651s autopkgtest [11:08:43]: testbed apt version: 2.9.14ubuntu1 651s autopkgtest [11:08:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 651s autopkgtest [11:08:43]: testbed release detected to be: None 652s autopkgtest [11:08:44]: updating testbed package index (apt update) 653s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 653s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 653s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 653s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 653s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [906 kB] 653s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 653s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.6 kB] 653s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.4 kB] 653s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [139 kB] 653s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [94.1 kB] 653s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB] 653s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B] 653s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [325 kB] 653s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB] 653s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6924 B] 653s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [22.7 kB] 654s Fetched 2546 kB in 1s (2301 kB/s) 654s Reading package lists... 655s Reading package lists... 655s Building dependency tree... 655s Reading state information... 656s Calculating upgrade... 656s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 656s Reading package lists... 656s Building dependency tree... 656s Reading state information... 657s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 657s autopkgtest [11:08:49]: upgrading testbed (apt dist-upgrade and autopurge) 657s Reading package lists... 657s Building dependency tree... 657s Reading state information... 658s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 658s Starting 2 pkgProblemResolver with broken count: 0 658s Done 659s Entering ResolveByKeep 659s 659s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 659s Reading package lists... 660s Building dependency tree... 660s Reading state information... 660s Starting pkgProblemResolver with broken count: 0 660s Starting 2 pkgProblemResolver with broken count: 0 660s Done 661s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 663s autopkgtest [11:08:55]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 663s autopkgtest [11:08:55]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 667s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (dsc) [2498 B] 667s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (tar) [11.9 MB] 667s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (diff) [11.6 kB] 667s gpgv: Signature made Fri Nov 15 13:41:43 2024 UTC 667s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 667s gpgv: Can't check signature: No public key 667s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build1.dsc: no acceptable signature found 667s autopkgtest [11:08:59]: testing package python-biom-format version 2.1.16-1build1 668s autopkgtest [11:09:00]: build not needed 670s autopkgtest [11:09:02]: test run-unit-test: preparing testbed 670s Reading package lists... 671s Building dependency tree... 671s Reading state information... 671s Starting pkgProblemResolver with broken count: 0 671s Starting 2 pkgProblemResolver with broken count: 0 671s Done 671s The following NEW packages will be installed: 671s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 671s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 671s libsz2 python-biom-format-doc python3-biom-format python3-click 671s python3-colorama python3-dateutil python3-decorator python3-h5py 671s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 671s python3-scipy python3-tz 672s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 672s Need to get 47.0 MB of archives. 672s After this operation, 260 MB of additional disk space will be used. 672s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 672s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 672s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 672s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 672s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 672s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 672s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 672s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 672s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 672s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 673s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 673s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 673s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biom-format-doc all 2.1.16-1build1 [57.9 kB] 673s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 673s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu3 [1689 kB] 673s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 673s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 673s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 673s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 673s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 673s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 674s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 674s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 674s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 674s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1build1 [186 kB] 675s Fetched 47.0 MB in 3s (15.8 MB/s) 675s Selecting previously unselected package libaec0:amd64. 675s (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 ... 75952 files and directories currently installed.) 675s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 675s Unpacking libaec0:amd64 (1.1.3-1) ... 675s Selecting previously unselected package libblas3:amd64. 675s Preparing to unpack .../01-libblas3_3.12.0-4_amd64.deb ... 675s Unpacking libblas3:amd64 (3.12.0-4) ... 675s Selecting previously unselected package libgfortran5:amd64. 675s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 675s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 675s Selecting previously unselected package libsz2:amd64. 675s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ... 675s Unpacking libsz2:amd64 (1.1.3-1) ... 675s Selecting previously unselected package libhdf5-103-1t64:amd64. 675s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 675s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 675s Selecting previously unselected package libhdf5-hl-100t64:amd64. 675s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 675s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 675s Selecting previously unselected package libjs-jquery. 675s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 675s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 675s Selecting previously unselected package libjs-underscore. 675s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 675s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 675s Selecting previously unselected package libjs-sphinxdoc. 675s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 675s Unpacking libjs-sphinxdoc (7.4.7-4) ... 675s Selecting previously unselected package liblapack3:amd64. 675s Preparing to unpack .../09-liblapack3_3.12.0-4_amd64.deb ... 675s Unpacking liblapack3:amd64 (3.12.0-4) ... 675s Selecting previously unselected package liblbfgsb0:amd64. 675s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 675s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 676s Selecting previously unselected package liblzf1:amd64. 676s Preparing to unpack .../11-liblzf1_3.6-4_amd64.deb ... 676s Unpacking liblzf1:amd64 (3.6-4) ... 676s Selecting previously unselected package python-biom-format-doc. 676s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build1_all.deb ... 676s Unpacking python-biom-format-doc (2.1.16-1build1) ... 676s Selecting previously unselected package python3-numpy. 676s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 676s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 676s Selecting previously unselected package python3-h5py-serial. 676s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu3_amd64.deb ... 676s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 676s Selecting previously unselected package python3-h5py. 676s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu3_all.deb ... 676s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 676s Selecting previously unselected package python3-colorama. 676s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 676s Unpacking python3-colorama (0.4.6-4) ... 676s Selecting previously unselected package python3-click. 676s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 676s Unpacking python3-click (8.1.7-2) ... 676s Selecting previously unselected package python3-dateutil. 676s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 676s Unpacking python3-dateutil (2.9.0-3) ... 676s Selecting previously unselected package python3-tz. 676s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 676s Unpacking python3-tz (2024.1-2) ... 676s Selecting previously unselected package python3-pandas-lib:amd64. 676s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_amd64.deb ... 676s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 676s Selecting previously unselected package python3-pandas. 676s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 676s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 677s Selecting previously unselected package python3-decorator. 677s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 677s Unpacking python3-decorator (5.1.1-5) ... 677s Selecting previously unselected package python3-scipy. 677s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 677s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 677s Selecting previously unselected package python3-biom-format. 677s Preparing to unpack .../24-python3-biom-format_2.1.16-1build1_amd64.deb ... 677s Unpacking python3-biom-format (2.1.16-1build1) ... 677s Setting up python3-colorama (0.4.6-4) ... 678s Setting up python3-click (8.1.7-2) ... 678s Setting up libaec0:amd64 (1.1.3-1) ... 678s Setting up python3-tz (2024.1-2) ... 678s Setting up python3-decorator (5.1.1-5) ... 678s Setting up libblas3:amd64 (3.12.0-4) ... 678s 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 678s Setting up liblzf1:amd64 (3.6-4) ... 678s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 678s Setting up python3-dateutil (2.9.0-3) ... 678s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 678s Setting up libsz2:amd64 (1.1.3-1) ... 678s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 678s Setting up liblapack3:amd64 (3.12.0-4) ... 678s 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 678s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 680s Setting up libjs-sphinxdoc (7.4.7-4) ... 680s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 680s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 680s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 680s Setting up python3-scipy (1.13.1-5ubuntu1) ... 682s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 682s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 683s Setting up python-biom-format-doc (2.1.16-1build1) ... 683s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 687s Setting up python3-h5py (3.11.0-8ubuntu3) ... 687s Setting up python3-biom-format (2.1.16-1build1) ... 687s Processing triggers for man-db (2.13.0-1) ... 688s Processing triggers for libc-bin (2.40-1ubuntu3) ... 689s autopkgtest [11:09:21]: test run-unit-test: [----------------------- 690s 690s System information 690s ================== 690s Platform: linux 690s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 690s Python executable: /usr/bin/python3 690s 690s Dependency versions 690s =================== 690s click version: 8.1.7 690s NumPy version: 1.26.4 690s SciPy version: 1.13.1 690s h5py version: 3.11.0 690s 690s biom-format package information 690s =============================== 690s biom-format version: 2.1.16 690s 690s 690s The input file is a valid BIOM-formatted file. 691s 691s The input file is a valid BIOM-formatted file. 692s 692s The input file is a valid BIOM-formatted file. 692s 692s The input file is a valid BIOM-formatted file. 694s + table=examples/min_sparse_otu_table_hdf5.biom 694s + obsmd=examples/obs_md.txt 694s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 694s + biom show-install-info 695s 695s System information 695s ================== 695s Platform: linux 695s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 695s Python executable: /usr/bin/python3 695s 695s Dependency versions 695s =================== 695s click version: 8.1.7 695s NumPy version: 1.26.4 695s SciPy version: 1.13.1 695s h5py version: 3.11.0 695s 695s biom-format package information 695s =============================== 695s biom-format version: 2.1.16 695s 695s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 695s 695s The input file is a valid BIOM-formatted file. 695s + 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 697s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 697s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 698s + biom validate-table -i test_json.biom 699s 699s The input file is a valid BIOM-formatted file. 699s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 699s + biom validate-table -i test_hdf5.biom 700s 700s The input file is a valid BIOM-formatted file. 700s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 701s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 701s + biom validate-table -i test_hdf5.biom 702s 702s The input file is a valid BIOM-formatted file. 702s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 703s + biom validate-table -i test_json.biom 703s 703s The input file is a valid BIOM-formatted file. 704s + biom head -i examples/min_sparse_otu_table_hdf5.biom 704s # Constructed from biom file 704s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 704s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 704s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 704s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 704s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 704s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 704s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 705s Sample1 705s Sample2 705s Sample3 705s Sample4 705s Sample5 705s Sample6 705s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 706s + cat 706s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 706s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 707s Num samples: 6 707s Num observations: 5 707s Total count: 27 707s Table density (fraction of non-zero values): 0.500 707s 707s Counts/sample summary: 707s Min: 3.000 707s Max: 7.000 707s Median: 4.000 707s Mean: 4.500 707s Std. dev.: 1.500 707s Sample Metadata Categories: None provided 707s Observation Metadata Categories: None provided 707s 707s Counts/sample detail: 707s Sample2: 3.000 707s Sample5: 3.000 707s Sample3: 4.000 707s Sample6: 4.000 707s Sample4: 6.000 707s Sample1: 7.000 707s + cat 707s + biom from-uc -i uctest -o test_uc.biom 708s If this message was shown, then all commands executed without failure 708s + echo If this message was shown, then all commands executed without failure 708s autopkgtest [11:09:40]: test run-unit-test: -----------------------] 709s autopkgtest [11:09:41]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 709s run-unit-test PASS 709s autopkgtest [11:09:41]: test autodep8-python3: preparing testbed 775s autopkgtest [11:10:47]: testbed dpkg architecture: amd64 775s autopkgtest [11:10:47]: testbed apt version: 2.9.14ubuntu1 776s autopkgtest [11:10:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 776s autopkgtest [11:10:48]: testbed release detected to be: plucky 777s autopkgtest [11:10:49]: updating testbed package index (apt update) 777s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 777s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 777s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 777s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 777s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.6 kB] 777s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.4 kB] 778s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 778s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [906 kB] 778s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [94.1 kB] 778s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [139 kB] 778s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2572 B] 778s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.6 kB] 778s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [831 kB] 778s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [325 kB] 778s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [22.7 kB] 778s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [6924 B] 778s Fetched 2546 kB in 1s (2178 kB/s) 779s Reading package lists... 780s Reading package lists... 780s Building dependency tree... 780s Reading state information... 781s Calculating upgrade... 781s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 781s Reading package lists... 781s Building dependency tree... 781s Reading state information... 781s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 781s autopkgtest [11:10:53]: upgrading testbed (apt dist-upgrade and autopurge) 782s Reading package lists... 782s Building dependency tree... 782s Reading state information... 782s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 782s Starting 2 pkgProblemResolver with broken count: 0 782s Done 783s Entering ResolveByKeep 783s 783s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 783s Reading package lists... 784s Building dependency tree... 784s Reading state information... 784s Starting pkgProblemResolver with broken count: 0 784s Starting 2 pkgProblemResolver with broken count: 0 784s Done 784s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 787s Reading package lists... 787s Building dependency tree... 787s Reading state information... 787s Starting pkgProblemResolver with broken count: 0 787s Starting 2 pkgProblemResolver with broken count: 0 787s Done 788s The following NEW packages will be installed: 788s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 788s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 788s python3-colorama python3-dateutil python3-decorator python3-h5py 788s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 788s python3-scipy python3-tz 789s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 789s Need to get 46.3 MB of archives. 789s After this operation, 258 MB of additional disk space will be used. 789s Get:1 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 789s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 789s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 789s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 789s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB] 789s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB] 789s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 790s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 790s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 790s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 790s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11ubuntu1 [5319 kB] 790s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py-serial amd64 3.11.0-8ubuntu3 [1689 kB] 791s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 791s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 791s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB] 791s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-3 [80.2 kB] 791s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB] 791s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5ubuntu1 [8271 kB] 791s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 791s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 791s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5ubuntu1 [21.7 MB] 792s Get:22 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1build1 [186 kB] 792s Fetched 46.3 MB in 4s (11.1 MB/s) 792s Selecting previously unselected package libaec0:amd64. 793s (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 ... 75952 files and directories currently installed.) 793s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 793s Unpacking libaec0:amd64 (1.1.3-1) ... 793s Selecting previously unselected package libblas3:amd64. 793s Preparing to unpack .../01-libblas3_3.12.0-4_amd64.deb ... 793s Unpacking libblas3:amd64 (3.12.0-4) ... 793s Selecting previously unselected package libgfortran5:amd64. 793s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 793s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 793s Selecting previously unselected package libsz2:amd64. 793s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ... 793s Unpacking libsz2:amd64 (1.1.3-1) ... 793s Selecting previously unselected package libhdf5-103-1t64:amd64. 793s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ... 793s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 793s Selecting previously unselected package libhdf5-hl-100t64:amd64. 793s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ... 793s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 793s Selecting previously unselected package liblapack3:amd64. 793s Preparing to unpack .../06-liblapack3_3.12.0-4_amd64.deb ... 793s Unpacking liblapack3:amd64 (3.12.0-4) ... 793s Selecting previously unselected package liblbfgsb0:amd64. 793s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 793s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 793s Selecting previously unselected package liblzf1:amd64. 793s Preparing to unpack .../08-liblzf1_3.6-4_amd64.deb ... 793s Unpacking liblzf1:amd64 (3.6-4) ... 793s Selecting previously unselected package python3-all. 793s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_amd64.deb ... 793s Unpacking python3-all (3.12.6-0ubuntu1) ... 793s Selecting previously unselected package python3-numpy. 793s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_amd64.deb ... 793s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 793s Selecting previously unselected package python3-h5py-serial. 793s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu3_amd64.deb ... 793s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 793s Selecting previously unselected package python3-h5py. 793s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu3_all.deb ... 793s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 793s Selecting previously unselected package python3-colorama. 793s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 793s Unpacking python3-colorama (0.4.6-4) ... 793s Selecting previously unselected package python3-click. 793s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 793s Unpacking python3-click (8.1.7-2) ... 793s Selecting previously unselected package python3-dateutil. 793s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 793s Unpacking python3-dateutil (2.9.0-3) ... 793s Selecting previously unselected package python3-tz. 793s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 793s Unpacking python3-tz (2024.1-2) ... 794s Selecting previously unselected package python3-pandas-lib:amd64. 794s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_amd64.deb ... 794s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 794s Selecting previously unselected package python3-pandas. 794s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 794s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 794s Selecting previously unselected package python3-decorator. 794s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 794s Unpacking python3-decorator (5.1.1-5) ... 794s Selecting previously unselected package python3-scipy. 794s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_amd64.deb ... 794s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 795s Selecting previously unselected package python3-biom-format. 795s Preparing to unpack .../21-python3-biom-format_2.1.16-1build1_amd64.deb ... 795s Unpacking python3-biom-format (2.1.16-1build1) ... 795s Setting up python3-colorama (0.4.6-4) ... 795s Setting up python3-all (3.12.6-0ubuntu1) ... 795s Setting up python3-click (8.1.7-2) ... 795s Setting up libaec0:amd64 (1.1.3-1) ... 795s Setting up python3-tz (2024.1-2) ... 795s Setting up python3-decorator (5.1.1-5) ... 795s Setting up libblas3:amd64 (3.12.0-4) ... 795s 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 795s Setting up liblzf1:amd64 (3.6-4) ... 795s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 795s Setting up python3-dateutil (2.9.0-3) ... 796s Setting up libsz2:amd64 (1.1.3-1) ... 796s Setting up liblapack3:amd64 (3.12.0-4) ... 796s 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 796s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 797s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ... 797s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 797s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ... 797s Setting up python3-scipy (1.13.1-5ubuntu1) ... 800s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5ubuntu1) ... 800s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 800s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 805s Setting up python3-h5py (3.11.0-8ubuntu3) ... 805s Setting up python3-biom-format (2.1.16-1build1) ... 805s Processing triggers for man-db (2.13.0-1) ... 805s Processing triggers for libc-bin (2.40-1ubuntu3) ... 810s autopkgtest [11:11:22]: 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 810s autopkgtest [11:11:22]: test autodep8-python3: [----------------------- 810s Testing with python3.12: 811s 811s autopkgtest [11:11:23]: test autodep8-python3: -----------------------] 812s autodep8-python3 PASS (superficial) 812s autopkgtest [11:11:24]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 812s autopkgtest [11:11:24]: @@@@@@@@@@@@@@@@@@@@ summary 812s run-unit-test PASS 812s autodep8-python3 PASS (superficial) 823s nova [W] Skipping flock for amd64 823s Creating nova instance adt-plucky-amd64-python-biom-format-20241202-105752-juju-7f2275-prod-proposed-migration-environment-15-2cf4d68a-839d-4d5e-aa0c-696f3aac6965 from image adt/ubuntu-plucky-amd64-server-20241202.img (UUID e2dd381a-9f8d-4c68-9282-8ccd9f59e142)... 823s nova [W] nova quota exceeded (attempt #0) 823s nova [W] nova quota exceeded (attempt #1) 823s nova [W] Skipping flock for amd64 823s Creating nova instance adt-plucky-amd64-python-biom-format-20241202-105752-juju-7f2275-prod-proposed-migration-environment-15-2cf4d68a-839d-4d5e-aa0c-696f3aac6965 from image adt/ubuntu-plucky-amd64-server-20241202.img (UUID e2dd381a-9f8d-4c68-9282-8ccd9f59e142)...