0s autopkgtest [16:33:24]: starting date and time: 2024-11-18 16:33:24+0000 0s autopkgtest [16:33:24]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [16:33:24]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lt4sk8lz/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,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 sphinx-rtd-theme/3.0.2+dfsg-1' -- lxd -r lxd-armhf-10.145.243.197 lxd-armhf-10.145.243.197:autopkgtest/ubuntu/plucky/armhf 54s autopkgtest [16:34:18]: testbed dpkg architecture: armhf 56s autopkgtest [16:34:20]: testbed apt version: 2.9.8 56s autopkgtest [16:34:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 66s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 66s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 66s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 66s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [79.6 kB] 66s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [584 kB] 66s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3240 B] 66s Fetched 1647 kB in 1s (1884 kB/s) 66s Reading package lists... 85s tee: /proc/self/fd/2: Permission denied 107s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 107s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 107s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 107s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 108s Reading package lists... 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 109s Calculating upgrade... 110s The following NEW packages will be installed: 110s liblsof0 110s The following packages will be upgraded: 110s lsof 110s 1 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 110s Need to get 300 kB of archives. 110s After this operation, 171 kB of additional disk space will be used. 110s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf liblsof0 armhf 4.99.3+dfsg-2 [60.5 kB] 110s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf lsof armhf 4.99.3+dfsg-2 [239 kB] 110s Fetched 300 kB in 1s (531 kB/s) 110s Selecting previously unselected package liblsof0. 111s (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 ... 59581 files and directories currently installed.) 111s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_armhf.deb ... 111s Unpacking liblsof0 (4.99.3+dfsg-2) ... 111s Preparing to unpack .../lsof_4.99.3+dfsg-2_armhf.deb ... 111s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 111s Setting up liblsof0 (4.99.3+dfsg-2) ... 111s Setting up lsof (4.99.3+dfsg-2) ... 111s Processing triggers for man-db (2.13.0-1) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [16:35:18]: rebooting testbed after setup commands that affected boot 184s autopkgtest [16:36:28]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 214s autopkgtest [16:36:58]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 231s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B] 231s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB] 231s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB] 231s gpgv: Signature made Mon May 27 20:43:46 2024 UTC 231s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 231s gpgv: issuer "emollier@debian.org" 231s gpgv: Can't check signature: No public key 231s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found 231s autopkgtest [16:37:15]: testing package python-biom-format version 2.1.16-1 234s autopkgtest [16:37:18]: build not needed 239s autopkgtest [16:37:23]: test run-unit-test: preparing testbed 253s Reading package lists... 253s Building dependency tree... 253s Reading state information... 253s Starting pkgProblemResolver with broken count: 0 253s Starting 2 pkgProblemResolver with broken count: 0 253s Done 254s The following additional packages will be installed: 254s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 254s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 254s libsz2 python-biom-format-doc python3-biom-format python3-click 254s python3-colorama python3-dateutil python3-decorator python3-h5py 254s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 254s python3-scipy python3-tz 254s Suggested packages: 254s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 254s python-pandas-doc python3-statsmodels python-scipy-doc 254s Recommended packages: 254s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 254s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 254s python3-tables g++ | c++-compiler python3-pil 254s The following NEW packages will be installed: 254s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 254s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 254s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 254s python3-click python3-colorama python3-dateutil python3-decorator 254s python3-h5py python3-h5py-serial python3-numpy python3-pandas 254s python3-pandas-lib python3-scipy python3-tz 254s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 254s Need to get 40.3 MB/40.3 MB of archives. 254s After this operation, 175 MB of additional disk space will be used. 254s Get:1 /tmp/autopkgtest.XCZQW0/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [720 B] 254s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 255s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 255s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 255s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 255s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 255s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 255s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 255s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 255s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 255s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 255s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 255s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 255s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biom-format-doc all 2.1.16-1 [57.5 kB] 255s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 255s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py-serial armhf 3.11.0-8ubuntu1 [1474 kB] 255s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py all 3.11.0-8ubuntu1 [7982 B] 255s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 255s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 255s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 255s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 255s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 255s Get:23 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 255s Get:24 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 255s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5ubuntu1 [19.1 MB] 256s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1 [135 kB] 256s Fetched 40.3 MB in 2s (25.5 MB/s) 256s Selecting previously unselected package libaec0:armhf. 256s (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 ... 59586 files and directories currently installed.) 256s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 256s Unpacking libaec0:armhf (1.1.3-1) ... 256s Selecting previously unselected package libblas3:armhf. 256s Preparing to unpack .../01-libblas3_3.12.0-3build2_armhf.deb ... 256s Unpacking libblas3:armhf (3.12.0-3build2) ... 256s Selecting previously unselected package libgfortran5:armhf. 256s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 256s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 256s Selecting previously unselected package libsz2:armhf. 256s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 256s Unpacking libsz2:armhf (1.1.3-1) ... 256s Selecting previously unselected package libhdf5-103-1t64:armhf. 256s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 256s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 256s Selecting previously unselected package libhdf5-hl-100t64:armhf. 256s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 256s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 257s Selecting previously unselected package libjs-jquery. 257s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 257s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 257s Selecting previously unselected package libjs-underscore. 257s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 257s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 257s Selecting previously unselected package libjs-sphinxdoc. 257s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 257s Unpacking libjs-sphinxdoc (7.4.7-4) ... 257s Selecting previously unselected package liblapack3:armhf. 257s Preparing to unpack .../09-liblapack3_3.12.0-3build2_armhf.deb ... 257s Unpacking liblapack3:armhf (3.12.0-3build2) ... 257s Selecting previously unselected package liblbfgsb0:armhf. 257s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 257s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 257s Selecting previously unselected package liblzf1:armhf. 257s Preparing to unpack .../11-liblzf1_3.6-4_armhf.deb ... 257s Unpacking liblzf1:armhf (3.6-4) ... 257s Selecting previously unselected package python-biom-format-doc. 257s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ... 257s Unpacking python-biom-format-doc (2.1.16-1) ... 257s Selecting previously unselected package python3-numpy. 257s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 257s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 257s Selecting previously unselected package python3-h5py-serial. 257s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu1_armhf.deb ... 257s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 257s Selecting previously unselected package python3-h5py. 257s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu1_all.deb ... 257s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 257s Selecting previously unselected package python3-colorama. 257s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 257s Unpacking python3-colorama (0.4.6-4) ... 257s Selecting previously unselected package python3-click. 257s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 257s Unpacking python3-click (8.1.7-2) ... 258s Selecting previously unselected package python3-dateutil. 258s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 258s Unpacking python3-dateutil (2.9.0-3) ... 258s Selecting previously unselected package python3-tz. 258s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 258s Unpacking python3-tz (2024.1-2) ... 258s Selecting previously unselected package python3-pandas-lib:armhf. 258s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 258s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 258s Selecting previously unselected package python3-pandas. 258s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 258s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 258s Selecting previously unselected package python3-decorator. 258s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 258s Unpacking python3-decorator (5.1.1-5) ... 258s Selecting previously unselected package python3-scipy. 258s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_armhf.deb ... 258s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 259s Selecting previously unselected package python3-biom-format. 259s Preparing to unpack .../24-python3-biom-format_2.1.16-1_armhf.deb ... 259s Unpacking python3-biom-format (2.1.16-1) ... 259s Selecting previously unselected package autopkgtest-satdep. 259s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 259s Unpacking autopkgtest-satdep (0) ... 259s Setting up python3-colorama (0.4.6-4) ... 259s Setting up python3-click (8.1.7-2) ... 259s Setting up libaec0:armhf (1.1.3-1) ... 259s Setting up python3-tz (2024.1-2) ... 260s Setting up python3-decorator (5.1.1-5) ... 260s Setting up libblas3:armhf (3.12.0-3build2) ... 260s 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 260s Setting up liblzf1:armhf (3.6-4) ... 260s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 260s Setting up python3-dateutil (2.9.0-3) ... 260s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 260s Setting up libsz2:armhf (1.1.3-1) ... 260s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 260s Setting up liblapack3:armhf (3.12.0-3build2) ... 260s 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 260s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 262s Setting up libjs-sphinxdoc (7.4.7-4) ... 262s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 262s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 262s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 262s Setting up python3-scipy (1.13.1-5ubuntu1) ... 266s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 266s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 266s Setting up python-biom-format-doc (2.1.16-1) ... 266s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 272s Setting up python3-h5py (3.11.0-8ubuntu1) ... 272s Setting up python3-biom-format (2.1.16-1) ... 273s Setting up autopkgtest-satdep (0) ... 273s Processing triggers for man-db (2.13.0-1) ... 273s Processing triggers for libc-bin (2.40-1ubuntu3) ... 289s (Reading database ... 64298 files and directories currently installed.) 289s Removing autopkgtest-satdep (0) ... 295s autopkgtest [16:38:19]: test run-unit-test: [----------------------- 298s 298s System information 298s ================== 298s Platform: linux 298s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 298s Python executable: /usr/bin/python3 298s 298s Dependency versions 298s =================== 298s click version: 8.1.7 298s NumPy version: 1.26.4 298s SciPy version: 1.13.1 298s h5py version: 3.11.0 298s 298s biom-format package information 298s =============================== 298s biom-format version: 2.1.16 298s 299s 299s The input file is a valid BIOM-formatted file. 300s 300s The input file is a valid BIOM-formatted file. 301s 301s The input file is a valid BIOM-formatted file. 302s 302s The input file is a valid BIOM-formatted file. 304s + table=examples/min_sparse_otu_table_hdf5.biom 304s + obsmd=examples/obs_md.txt 304s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 304s + biom show-install-info 304s 304s System information 304s ================== 304s Platform: linux 304s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 304s Python executable: /usr/bin/python3 304s 304s Dependency versions 304s =================== 304s click version: 8.1.7 304s NumPy version: 1.26.4 304s SciPy version: 1.13.1 304s h5py version: 3.11.0 304s 304s biom-format package information 304s =============================== 304s biom-format version: 2.1.16 304s 305s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 305s 305s The input file is a valid BIOM-formatted file. 306s + 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 307s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 308s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 309s + biom validate-table -i test_json.biom 309s 309s The input file is a valid BIOM-formatted file. 309s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 310s + biom validate-table -i test_hdf5.biom 311s 311s The input file is a valid BIOM-formatted file. 311s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 312s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 313s + biom validate-table -i test_hdf5.biom 314s 314s The input file is a valid BIOM-formatted file. 314s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 315s + biom validate-table -i test_json.biom 316s 316s The input file is a valid BIOM-formatted file. 316s + biom head -i examples/min_sparse_otu_table_hdf5.biom 317s # Constructed from biom file 317s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 317s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 317s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 317s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 317s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 317s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 317s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 318s Sample1 318s Sample2 318s Sample3 318s Sample4 318s Sample5 318s Sample6 318s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 319s + cat 319s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 320s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 321s Num samples: 6 321s Num observations: 5 321s Total count: 27 321s Table density (fraction of non-zero values): 0.500 321s 321s Counts/sample summary: 321s Min: 3.000 321s Max: 7.000 321s Median: 4.000 321s Mean: 4.500 321s Std. dev.: 1.500 321s Sample Metadata Categories: None provided 321s Observation Metadata Categories: None provided 321s 321s Counts/sample detail: 321s Sample2: 3.000 321s Sample5: 3.000 321s Sample3: 4.000 321s Sample6: 4.000 321s Sample4: 6.000 321s Sample1: 7.000 321s + cat 321s + biom from-uc -i uctest -o test_uc.biom 322s + echo If this message was shown, then all commands executed without failure 322s If this message was shown, then all commands executed without failure 323s autopkgtest [16:38:47]: test run-unit-test: -----------------------] 327s autopkgtest [16:38:51]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 327s run-unit-test PASS 331s autopkgtest [16:38:55]: test autodep8-python3: preparing testbed 384s autopkgtest [16:39:48]: testbed dpkg architecture: armhf 386s autopkgtest [16:39:50]: testbed apt version: 2.9.8 386s autopkgtest [16:39:50]: @@@@@@@@@@@@@@@@@@@@ test bed setup 394s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 394s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [814 kB] 394s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [71.7 kB] 394s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 394s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 394s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [79.6 kB] 394s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [584 kB] 394s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3240 B] 394s Fetched 1647 kB in 1s (1846 kB/s) 394s Reading package lists... 410s tee: /proc/self/fd/2: Permission denied 432s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 432s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 432s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 432s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 433s Reading package lists... 434s Reading package lists... 434s Building dependency tree... 434s Reading state information... 434s Calculating upgrade... 435s The following NEW packages will be installed: 435s liblsof0 435s The following packages will be upgraded: 435s lsof 435s 1 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 435s Need to get 300 kB of archives. 435s After this operation, 171 kB of additional disk space will be used. 435s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf liblsof0 armhf 4.99.3+dfsg-2 [60.5 kB] 435s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf lsof armhf 4.99.3+dfsg-2 [239 kB] 436s Fetched 300 kB in 0s (631 kB/s) 436s Selecting previously unselected package liblsof0. 436s (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 ... 59581 files and directories currently installed.) 436s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_armhf.deb ... 436s Unpacking liblsof0 (4.99.3+dfsg-2) ... 436s Preparing to unpack .../lsof_4.99.3+dfsg-2_armhf.deb ... 436s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 436s Setting up liblsof0 (4.99.3+dfsg-2) ... 436s Setting up lsof (4.99.3+dfsg-2) ... 436s Processing triggers for man-db (2.13.0-1) ... 436s Processing triggers for libc-bin (2.40-1ubuntu3) ... 437s Reading package lists... 437s Building dependency tree... 437s Reading state information... 438s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 440s autopkgtest [16:40:44]: rebooting testbed after setup commands that affected boot 537s Reading package lists... 537s Building dependency tree... 537s Reading state information... 538s Starting pkgProblemResolver with broken count: 0 538s Starting 2 pkgProblemResolver with broken count: 0 538s Done 539s The following additional packages will be installed: 539s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 539s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 539s python3-colorama python3-dateutil python3-decorator python3-h5py 539s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 539s python3-scipy python3-tz 539s Suggested packages: 539s python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc 539s python3-dev python3-pytest python-pandas-doc python3-statsmodels 539s python-scipy-doc 539s Recommended packages: 539s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 539s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 539s g++ | c++-compiler python3-pil 539s The following NEW packages will be installed: 539s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 539s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all 539s python3-biom-format python3-click python3-colorama python3-dateutil 539s python3-decorator python3-h5py python3-h5py-serial python3-numpy 539s python3-pandas python3-pandas-lib python3-scipy python3-tz 539s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 539s Need to get 39.6 MB/39.6 MB of archives. 539s After this operation, 173 MB of additional disk space will be used. 539s Get:1 /tmp/autopkgtest.XCZQW0/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [716 B] 539s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 539s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 539s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 539s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 539s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 539s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 539s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 539s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 539s Get:10 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 539s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.12.6-0ubuntu1 [886 B] 539s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11ubuntu1 [3975 kB] 540s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py-serial armhf 3.11.0-8ubuntu1 [1474 kB] 540s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-h5py all 3.11.0-8ubuntu1 [7982 B] 540s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 540s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 540s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 540s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 540s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5ubuntu1 [7608 kB] 540s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 540s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 540s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5ubuntu1 [19.1 MB] 541s Get:23 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1 [135 kB] 541s Fetched 39.6 MB in 2s (20.4 MB/s) 541s Selecting previously unselected package libaec0:armhf. 541s (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 ... 59586 files and directories currently installed.) 541s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 541s Unpacking libaec0:armhf (1.1.3-1) ... 541s Selecting previously unselected package libblas3:armhf. 541s Preparing to unpack .../01-libblas3_3.12.0-3build2_armhf.deb ... 541s Unpacking libblas3:armhf (3.12.0-3build2) ... 541s Selecting previously unselected package libgfortran5:armhf. 541s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 541s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 541s Selecting previously unselected package libsz2:armhf. 541s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 541s Unpacking libsz2:armhf (1.1.3-1) ... 541s Selecting previously unselected package libhdf5-103-1t64:armhf. 541s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 541s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 541s Selecting previously unselected package libhdf5-hl-100t64:armhf. 541s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 541s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 541s Selecting previously unselected package liblapack3:armhf. 541s Preparing to unpack .../06-liblapack3_3.12.0-3build2_armhf.deb ... 541s Unpacking liblapack3:armhf (3.12.0-3build2) ... 541s Selecting previously unselected package liblbfgsb0:armhf. 541s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 541s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 541s Selecting previously unselected package liblzf1:armhf. 541s Preparing to unpack .../08-liblzf1_3.6-4_armhf.deb ... 541s Unpacking liblzf1:armhf (3.6-4) ... 541s Selecting previously unselected package python3-all. 541s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_armhf.deb ... 541s Unpacking python3-all (3.12.6-0ubuntu1) ... 541s Selecting previously unselected package python3-numpy. 541s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_armhf.deb ... 541s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 542s Selecting previously unselected package python3-h5py-serial. 542s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu1_armhf.deb ... 542s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 542s Selecting previously unselected package python3-h5py. 542s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu1_all.deb ... 542s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 542s Selecting previously unselected package python3-colorama. 542s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 542s Unpacking python3-colorama (0.4.6-4) ... 542s Selecting previously unselected package python3-click. 542s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 542s Unpacking python3-click (8.1.7-2) ... 542s Selecting previously unselected package python3-dateutil. 542s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 542s Unpacking python3-dateutil (2.9.0-3) ... 542s Selecting previously unselected package python3-tz. 542s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 542s Unpacking python3-tz (2024.1-2) ... 542s Selecting previously unselected package python3-pandas-lib:armhf. 542s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_armhf.deb ... 542s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 542s Selecting previously unselected package python3-pandas. 542s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 542s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 543s Selecting previously unselected package python3-decorator. 543s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 543s Unpacking python3-decorator (5.1.1-5) ... 543s Selecting previously unselected package python3-scipy. 543s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_armhf.deb ... 543s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 543s Selecting previously unselected package python3-biom-format. 543s Preparing to unpack .../21-python3-biom-format_2.1.16-1_armhf.deb ... 543s Unpacking python3-biom-format (2.1.16-1) ... 543s Selecting previously unselected package autopkgtest-satdep. 543s Preparing to unpack .../22-2-autopkgtest-satdep.deb ... 543s Unpacking autopkgtest-satdep (0) ... 543s Setting up python3-colorama (0.4.6-4) ... 543s Setting up python3-all (3.12.6-0ubuntu1) ... 543s Setting up python3-click (8.1.7-2) ... 544s Setting up libaec0:armhf (1.1.3-1) ... 544s Setting up python3-tz (2024.1-2) ... 544s Setting up python3-decorator (5.1.1-5) ... 544s Setting up libblas3:armhf (3.12.0-3build2) ... 544s 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 544s Setting up liblzf1:armhf (3.6-4) ... 544s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 544s Setting up python3-dateutil (2.9.0-3) ... 544s Setting up libsz2:armhf (1.1.3-1) ... 544s Setting up liblapack3:armhf (3.12.0-3build2) ... 544s 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 544s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 546s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 546s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 546s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 546s Setting up python3-scipy (1.13.1-5ubuntu1) ... 550s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5ubuntu1) ... 550s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 550s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 557s Setting up python3-h5py (3.11.0-8ubuntu1) ... 557s Setting up python3-biom-format (2.1.16-1) ... 557s Setting up autopkgtest-satdep (0) ... 557s Processing triggers for man-db (2.13.0-1) ... 558s Processing triggers for libc-bin (2.40-1ubuntu3) ... 571s (Reading database ... 64200 files and directories currently installed.) 571s Removing autopkgtest-satdep (0) ... 584s autopkgtest [16:43:08]: 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 584s autopkgtest [16:43:08]: test autodep8-python3: [----------------------- 585s Testing with python3.12: 586s 587s autopkgtest [16:43:11]: test autodep8-python3: -----------------------] 591s autopkgtest [16:43:15]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 591s autodep8-python3 PASS (superficial) 594s autopkgtest [16:43:18]: @@@@@@@@@@@@@@@@@@@@ summary 594s run-unit-test PASS 594s autodep8-python3 PASS (superficial)