0s autopkgtest [11:02:53]: starting date and time: 2024-12-02 11:02:53+0000 0s autopkgtest [11:02:53]: git checkout: be626eda Fix armhf LXD image generation for plucky 0s autopkgtest [11:02:53]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lyvl03lm/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:h5py --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu3 -- lxd -r lxd-armhf-10.145.243.149 lxd-armhf-10.145.243.149:autopkgtest/ubuntu/plucky/armhf 61s autopkgtest [11:03:54]: testbed dpkg architecture: armhf 65s autopkgtest [11:03:57]: testbed apt version: 2.9.14ubuntu1 71s autopkgtest [11:04:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 74s autopkgtest [11:04:07]: testbed release detected to be: None 87s autopkgtest [11:04:20]: updating testbed package index (apt update) 91s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 91s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 91s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 91s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 91s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.6 kB] 91s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.4 kB] 91s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 91s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [906 kB] 91s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [100 kB] 91s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [928 B] 91s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [744 kB] 91s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [8344 B] 91s Get:13 http://ftpmaster.internal/ubuntu plucky/main Sources [1377 kB] 92s Get:14 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.7 MB] 93s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [298 kB] 93s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1353 kB] 94s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.0 MB] 94s Get:18 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [174 kB] 98s Fetched 41.0 MB in 7s (5965 kB/s) 99s Reading package lists... 107s autopkgtest [11:04:40]: upgrading testbed (apt dist-upgrade and autopurge) 109s Reading package lists... 109s Building dependency tree... 109s Reading state information... 110s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 110s Starting 2 pkgProblemResolver with broken count: 0 110s Done 111s Entering ResolveByKeep 111s 112s The following packages will be upgraded: 112s fwupd libfwupd3 python3-software-properties software-properties-common 112s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 5190 kB of archives. 112s After this operation, 4096 B disk space will be freed. 112s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.2-2 [5020 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.2-2 [124 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.107 [16.5 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.107 [30.4 kB] 114s Fetched 5190 kB in 1s (3644 kB/s) 114s (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 ... 59970 files and directories currently installed.) 114s Preparing to unpack .../fwupd_2.0.2-2_armhf.deb ... 114s Unpacking fwupd (2.0.2-2) over (2.0.2-1) ... 114s Preparing to unpack .../libfwupd3_2.0.2-2_armhf.deb ... 114s Unpacking libfwupd3:armhf (2.0.2-2) over (2.0.2-1) ... 114s Preparing to unpack .../software-properties-common_0.107_all.deb ... 115s Unpacking software-properties-common (0.107) over (0.105) ... 115s Preparing to unpack .../python3-software-properties_0.107_all.deb ... 115s Unpacking python3-software-properties (0.107) over (0.105) ... 115s Setting up libfwupd3:armhf (2.0.2-2) ... 115s Setting up python3-software-properties (0.107) ... 115s Setting up fwupd (2.0.2-2) ... 116s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 116s fwupd.service is a disabled or a static unit not running, not starting it. 116s Setting up software-properties-common (0.107) ... 116s Processing triggers for libc-bin (2.40-1ubuntu3) ... 116s Processing triggers for man-db (2.13.0-1) ... 117s Processing triggers for dbus (1.14.10-4ubuntu5) ... 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 120s Starting pkgProblemResolver with broken count: 0 120s Starting 2 pkgProblemResolver with broken count: 0 120s Done 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [11:04:57]: rebooting testbed after setup commands that affected boot 205s autopkgtest [11:06:18]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 239s autopkgtest [11:06:52]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 260s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (dsc) [2498 B] 260s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (tar) [11.9 MB] 260s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (diff) [11.6 kB] 260s gpgv: Signature made Fri Nov 15 13:41:43 2024 UTC 260s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 260s gpgv: Can't check signature: No public key 260s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build1.dsc: no acceptable signature found 261s autopkgtest [11:07:14]: testing package python-biom-format version 2.1.16-1build1 264s autopkgtest [11:07:17]: build not needed 269s autopkgtest [11:07:22]: test run-unit-test: preparing testbed 272s Reading package lists... 272s Building dependency tree... 272s Reading state information... 272s Starting pkgProblemResolver with broken count: 0 272s Starting 2 pkgProblemResolver with broken count: 0 272s Done 273s The following NEW packages will be installed: 273s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 273s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 273s libsz2 python-biom-format-doc python3-biom-format python3-click 273s python3-colorama python3-dateutil python3-decorator python3-h5py 273s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 273s python3-scipy python3-tz 273s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 273s Need to get 40.4 MB of archives. 273s After this operation, 175 MB of additional disk space will be used. 273s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 274s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-4 [126 kB] 274s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 274s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 274s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 274s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 274s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 274s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 274s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 274s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-4 [2086 kB] 274s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 274s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 274s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biom-format-doc all 2.1.16-1build1 [57.9 kB] 274s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 275s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py-serial armhf 3.11.0-8ubuntu3 [1559 kB] 275s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py all 3.11.0-8ubuntu3 [7982 B] 275s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 275s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 275s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 275s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 275s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 275s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 275s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 275s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5ubuntu1 [19.1 MB] 276s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1build1 [157 kB] 276s Fetched 40.4 MB in 3s (14.7 MB/s) 277s Selecting previously unselected package libaec0:armhf. 277s (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 ... 59970 files and directories currently installed.) 277s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 277s Unpacking libaec0:armhf (1.1.3-1) ... 277s Selecting previously unselected package libblas3:armhf. 277s Preparing to unpack .../01-libblas3_3.12.0-4_armhf.deb ... 277s Unpacking libblas3:armhf (3.12.0-4) ... 277s Selecting previously unselected package libgfortran5:armhf. 277s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 277s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 277s Selecting previously unselected package libsz2:armhf. 277s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 277s Unpacking libsz2:armhf (1.1.3-1) ... 277s Selecting previously unselected package libhdf5-103-1t64:armhf. 277s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 277s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 277s Selecting previously unselected package libhdf5-hl-100t64:armhf. 277s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 277s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 277s Selecting previously unselected package libjs-jquery. 277s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 277s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 277s Selecting previously unselected package libjs-underscore. 277s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 277s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 277s Selecting previously unselected package libjs-sphinxdoc. 277s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 277s Unpacking libjs-sphinxdoc (7.4.7-4) ... 277s Selecting previously unselected package liblapack3:armhf. 277s Preparing to unpack .../09-liblapack3_3.12.0-4_armhf.deb ... 277s Unpacking liblapack3:armhf (3.12.0-4) ... 277s Selecting previously unselected package liblbfgsb0:armhf. 277s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 277s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 277s Selecting previously unselected package liblzf1:armhf. 277s Preparing to unpack .../11-liblzf1_3.6-4_armhf.deb ... 277s Unpacking liblzf1:armhf (3.6-4) ... 277s Selecting previously unselected package python-biom-format-doc. 277s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build1_all.deb ... 277s Unpacking python-biom-format-doc (2.1.16-1build1) ... 277s Selecting previously unselected package python3-numpy. 277s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 277s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 277s Selecting previously unselected package python3-h5py-serial. 277s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu3_armhf.deb ... 277s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 277s Selecting previously unselected package python3-h5py. 277s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu3_all.deb ... 277s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 278s Selecting previously unselected package python3-colorama. 278s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 278s Unpacking python3-colorama (0.4.6-4) ... 278s Selecting previously unselected package python3-click. 278s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 278s Unpacking python3-click (8.1.7-2) ... 278s Selecting previously unselected package python3-dateutil. 278s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 278s Unpacking python3-dateutil (2.9.0-3) ... 278s Selecting previously unselected package python3-tz. 278s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 278s Unpacking python3-tz (2024.1-2) ... 278s Selecting previously unselected package python3-pandas-lib:armhf. 278s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 278s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 278s Selecting previously unselected package python3-pandas. 278s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 278s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 278s Selecting previously unselected package python3-decorator. 278s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 278s Unpacking python3-decorator (5.1.1-5) ... 278s Selecting previously unselected package python3-scipy. 278s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_armhf.deb ... 278s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 279s Selecting previously unselected package python3-biom-format. 279s Preparing to unpack .../24-python3-biom-format_2.1.16-1build1_armhf.deb ... 279s Unpacking python3-biom-format (2.1.16-1build1) ... 279s Setting up python3-colorama (0.4.6-4) ... 279s Setting up python3-click (8.1.7-2) ... 279s Setting up libaec0:armhf (1.1.3-1) ... 279s Setting up python3-tz (2024.1-2) ... 279s Setting up python3-decorator (5.1.1-5) ... 280s Setting up libblas3:armhf (3.12.0-4) ... 280s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 280s Setting up liblzf1:armhf (3.6-4) ... 280s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 280s Setting up python3-dateutil (2.9.0-3) ... 280s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 280s Setting up libsz2:armhf (1.1.3-1) ... 280s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 280s Setting up liblapack3:armhf (3.12.0-4) ... 280s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 280s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 282s Setting up libjs-sphinxdoc (7.4.7-4) ... 282s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 282s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 282s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 282s Setting up python3-scipy (1.13.1-5ubuntu1) ... 286s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 286s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 286s Setting up python-biom-format-doc (2.1.16-1build1) ... 286s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 292s Setting up python3-h5py (3.11.0-8ubuntu3) ... 292s Setting up python3-biom-format (2.1.16-1build1) ... 293s Processing triggers for man-db (2.13.0-1) ... 293s Processing triggers for libc-bin (2.40-1ubuntu3) ... 306s autopkgtest [11:07:59]: test run-unit-test: [----------------------- 309s 309s System information 309s ================== 309s Platform: linux 309s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 309s Python executable: /usr/bin/python3 309s 309s Dependency versions 309s =================== 309s click version: 8.1.7 309s NumPy version: 1.26.4 309s SciPy version: 1.13.1 309s h5py version: 3.11.0 309s 309s biom-format package information 309s =============================== 309s biom-format version: 2.1.16 309s 310s 310s The input file is a valid BIOM-formatted file. 311s 311s The input file is a valid BIOM-formatted file. 312s 312s The input file is a valid BIOM-formatted file. 314s 314s The input file is a valid BIOM-formatted file. 316s + table=examples/min_sparse_otu_table_hdf5.biom 316s + obsmd=examples/obs_md.txt 316s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 316s + biom show-install-info 317s 317s System information 317s ================== 317s Platform: linux 317s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 317s Python executable: /usr/bin/python3 317s 317s Dependency versions 317s =================== 317s click version: 8.1.7 317s NumPy version: 1.26.4 317s SciPy version: 1.13.1 317s h5py version: 3.11.0 317s 317s biom-format package information 317s =============================== 317s biom-format version: 2.1.16 317s 317s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 318s 318s The input file is a valid BIOM-formatted file. 318s + 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 319s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 320s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 321s + biom validate-table -i test_json.biom 322s 322s The input file is a valid BIOM-formatted file. 322s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 323s + biom validate-table -i test_hdf5.biom 324s 324s The input file is a valid BIOM-formatted file. 324s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 325s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 326s + biom validate-table -i test_hdf5.biom 327s 327s The input file is a valid BIOM-formatted file. 328s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 329s + biom validate-table -i test_json.biom 330s 330s The input file is a valid BIOM-formatted file. 330s + biom head -i examples/min_sparse_otu_table_hdf5.biom 331s # Constructed from biom file 331s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 331s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 331s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 331s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 331s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 331s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 331s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 332s Sample1 332s Sample2 332s Sample3 332s Sample4 332s Sample5 332s Sample6 332s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 333s + cat 333s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 334s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 335s Num samples: 6 335s Num observations: 5 335s Total count: 27 335s Table density (fraction of non-zero values): 0.500 335s 335s Counts/sample summary: 335s Min: 3.000 335s Max: 7.000 335s Median: 4.000 335s Mean: 4.500 335s Std. dev.: 1.500 335s Sample Metadata Categories: None provided 335s Observation Metadata Categories: None provided 335s 335s Counts/sample detail: 335s Sample2: 3.000 335s Sample5: 3.000 335s Sample3: 4.000 335s Sample6: 4.000 335s Sample4: 6.000 335s Sample1: 7.000 335s + cat 335s + biom from-uc -i uctest -o test_uc.biom 336s If this message was shown, then all commands executed without failure 336s + echo If this message was shown, then all commands executed without failure 337s autopkgtest [11:08:30]: test run-unit-test: -----------------------] 342s autopkgtest [11:08:35]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 342s run-unit-test PASS 348s autopkgtest [11:08:41]: test autodep8-python3: preparing testbed 404s autopkgtest [11:09:37]: testbed dpkg architecture: armhf 407s autopkgtest [11:09:40]: testbed apt version: 2.9.14ubuntu1 412s autopkgtest [11:09:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 415s autopkgtest [11:09:48]: testbed release detected to be: plucky 425s autopkgtest [11:09:58]: updating testbed package index (apt update) 427s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 428s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [213 kB] 428s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 428s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 428s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [78.6 kB] 428s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [906 kB] 429s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.4 kB] 429s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 429s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [100 kB] 429s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [928 B] 429s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [744 kB] 429s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [8344 B] 429s Get:13 http://ftpmaster.internal/ubuntu plucky/main Sources [1377 kB] 430s Get:14 http://ftpmaster.internal/ubuntu plucky/universe Sources [20.7 MB] 433s Get:15 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [298 kB] 433s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1353 kB] 433s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.0 MB] 434s Get:18 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [174 kB] 437s Fetched 41.0 MB in 9s (4412 kB/s) 438s Reading package lists... 445s autopkgtest [11:10:18]: upgrading testbed (apt dist-upgrade and autopurge) 447s Reading package lists... 447s Building dependency tree... 447s Reading state information... 448s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 448s Starting 2 pkgProblemResolver with broken count: 0 448s Done 449s Entering ResolveByKeep 449s 450s The following packages will be upgraded: 450s fwupd libfwupd3 python3-software-properties software-properties-common 450s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 450s Need to get 5190 kB of archives. 450s After this operation, 4096 B disk space will be freed. 450s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf fwupd armhf 2.0.2-2 [5020 kB] 451s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libfwupd3 armhf 2.0.2-2 [124 kB] 451s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf software-properties-common all 0.107 [16.5 kB] 451s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf python3-software-properties all 0.107 [30.4 kB] 451s Fetched 5190 kB in 1s (5963 kB/s) 451s (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 ... 59970 files and directories currently installed.) 451s Preparing to unpack .../fwupd_2.0.2-2_armhf.deb ... 451s Unpacking fwupd (2.0.2-2) over (2.0.2-1) ... 451s Preparing to unpack .../libfwupd3_2.0.2-2_armhf.deb ... 451s Unpacking libfwupd3:armhf (2.0.2-2) over (2.0.2-1) ... 452s Preparing to unpack .../software-properties-common_0.107_all.deb ... 452s Unpacking software-properties-common (0.107) over (0.105) ... 452s Preparing to unpack .../python3-software-properties_0.107_all.deb ... 452s Unpacking python3-software-properties (0.107) over (0.105) ... 452s Setting up libfwupd3:armhf (2.0.2-2) ... 452s Setting up python3-software-properties (0.107) ... 452s Setting up fwupd (2.0.2-2) ... 452s fwupd-refresh.service is a disabled or a static unit not running, not starting it. 453s fwupd.service is a disabled or a static unit not running, not starting it. 453s Setting up software-properties-common (0.107) ... 453s Processing triggers for libc-bin (2.40-1ubuntu3) ... 453s Processing triggers for man-db (2.13.0-1) ... 454s Processing triggers for dbus (1.14.10-4ubuntu5) ... 456s Reading package lists... 457s Building dependency tree... 457s Reading state information... 457s Starting pkgProblemResolver with broken count: 0 457s Starting 2 pkgProblemResolver with broken count: 0 457s Done 458s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 461s autopkgtest [11:10:34]: rebooting testbed after setup commands that affected boot 569s Reading package lists... 569s Building dependency tree... 569s Reading state information... 570s Starting pkgProblemResolver with broken count: 0 570s Starting 2 pkgProblemResolver with broken count: 0 570s Done 570s The following NEW packages will be installed: 570s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 570s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 570s python3-colorama python3-dateutil python3-decorator python3-h5py 570s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 570s python3-scipy python3-tz 571s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 571s Need to get 39.7 MB of archives. 571s After this operation, 173 MB of additional disk space will be used. 571s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 571s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-4 [126 kB] 571s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 571s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 571s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 571s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 571s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-4 [2086 kB] 571s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 571s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 571s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 571s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 571s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py-serial armhf 3.11.0-8ubuntu3 [1559 kB] 571s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py all 3.11.0-8ubuntu3 [7982 B] 571s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 571s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 571s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 571s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 571s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 572s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 572s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 572s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5ubuntu1 [19.1 MB] 572s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1build1 [157 kB] 573s Fetched 39.7 MB in 2s (22.6 MB/s) 573s Selecting previously unselected package libaec0:armhf. 573s (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 ... 59970 files and directories currently installed.) 573s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 573s Unpacking libaec0:armhf (1.1.3-1) ... 573s Selecting previously unselected package libblas3:armhf. 573s Preparing to unpack .../01-libblas3_3.12.0-4_armhf.deb ... 573s Unpacking libblas3:armhf (3.12.0-4) ... 573s Selecting previously unselected package libgfortran5:armhf. 573s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 573s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 573s Selecting previously unselected package libsz2:armhf. 573s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 573s Unpacking libsz2:armhf (1.1.3-1) ... 573s Selecting previously unselected package libhdf5-103-1t64:armhf. 573s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 573s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 573s Selecting previously unselected package libhdf5-hl-100t64:armhf. 573s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 573s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 573s Selecting previously unselected package liblapack3:armhf. 573s Preparing to unpack .../06-liblapack3_3.12.0-4_armhf.deb ... 573s Unpacking liblapack3:armhf (3.12.0-4) ... 573s Selecting previously unselected package liblbfgsb0:armhf. 573s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 573s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 573s Selecting previously unselected package liblzf1:armhf. 573s Preparing to unpack .../08-liblzf1_3.6-4_armhf.deb ... 573s Unpacking liblzf1:armhf (3.6-4) ... 574s Selecting previously unselected package python3-all. 574s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_armhf.deb ... 574s Unpacking python3-all (3.12.6-0ubuntu1) ... 574s Selecting previously unselected package python3-numpy. 574s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 574s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 574s Selecting previously unselected package python3-h5py-serial. 574s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu3_armhf.deb ... 574s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 574s Selecting previously unselected package python3-h5py. 574s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu3_all.deb ... 574s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 574s Selecting previously unselected package python3-colorama. 574s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 574s Unpacking python3-colorama (0.4.6-4) ... 574s Selecting previously unselected package python3-click. 574s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 574s Unpacking python3-click (8.1.7-2) ... 574s Selecting previously unselected package python3-dateutil. 574s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 574s Unpacking python3-dateutil (2.9.0-3) ... 574s Selecting previously unselected package python3-tz. 574s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 574s Unpacking python3-tz (2024.1-2) ... 574s Selecting previously unselected package python3-pandas-lib:armhf. 574s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 574s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 574s Selecting previously unselected package python3-pandas. 574s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 574s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 574s Selecting previously unselected package python3-decorator. 574s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 574s Unpacking python3-decorator (5.1.1-5) ... 574s Selecting previously unselected package python3-scipy. 574s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_armhf.deb ... 574s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 575s Selecting previously unselected package python3-biom-format. 575s Preparing to unpack .../21-python3-biom-format_2.1.16-1build1_armhf.deb ... 575s Unpacking python3-biom-format (2.1.16-1build1) ... 575s Setting up python3-colorama (0.4.6-4) ... 575s Setting up python3-all (3.12.6-0ubuntu1) ... 575s Setting up python3-click (8.1.7-2) ... 575s Setting up libaec0:armhf (1.1.3-1) ... 575s Setting up python3-tz (2024.1-2) ... 575s Setting up python3-decorator (5.1.1-5) ... 576s Setting up libblas3:armhf (3.12.0-4) ... 576s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 576s Setting up liblzf1:armhf (3.6-4) ... 576s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 576s Setting up python3-dateutil (2.9.0-3) ... 576s Setting up libsz2:armhf (1.1.3-1) ... 576s Setting up liblapack3:armhf (3.12.0-4) ... 576s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 576s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 578s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 578s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 578s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 578s Setting up python3-scipy (1.13.1-5ubuntu1) ... 582s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 582s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 582s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 588s Setting up python3-h5py (3.11.0-8ubuntu3) ... 588s Setting up python3-biom-format (2.1.16-1build1) ... 588s Processing triggers for man-db (2.13.0-1) ... 588s Processing triggers for libc-bin (2.40-1ubuntu3) ... 607s autopkgtest [11:13:00]: 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 607s autopkgtest [11:13:00]: test autodep8-python3: [----------------------- 610s Testing with python3.12: 611s 611s autopkgtest [11:13:04]: test autodep8-python3: -----------------------] 616s autodep8-python3 PASS (superficial) 616s autopkgtest [11:13:09]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 621s autopkgtest [11:13:14]: @@@@@@@@@@@@@@@@@@@@ summary 621s run-unit-test PASS 621s autodep8-python3 PASS (superficial)