0s autopkgtest [23:23:55]: starting date and time: 2024-11-18 23:23:55+0000 0s autopkgtest [23:23:55]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [23:23:55]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.xds22isl/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-ppc64el-21.secgroup --name adt-plucky-ppc64el-python-biom-format-20241118-232355-juju-7f2275-prod-proposed-migration-environment-20-e5401589-ecf1-433f-bce0-7be4c70ace98 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -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/ 87s autopkgtest [23:25:22]: testbed dpkg architecture: ppc64el 87s autopkgtest [23:25:22]: testbed apt version: 2.9.8 87s autopkgtest [23:25:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.1 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [817 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 89s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [87.5 kB] 89s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [621 kB] 89s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [6788 B] 89s Fetched 1699 kB in 1s (2025 kB/s) 89s Reading package lists... 91s Reading package lists... 92s Building dependency tree... 92s Reading state information... 92s Calculating upgrade... 92s The following NEW packages will be installed: 92s liblsof0 92s The following packages will be upgraded: 92s linux-firmware lsof 92s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 92s Need to get 538 MB of archives. 92s After this operation, 1614 kB of additional disk space will be used. 92s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsof0 ppc64el 4.99.3+dfsg-2 [68.1 kB] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el lsof ppc64el 4.99.3+dfsg-2 [255 kB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el linux-firmware ppc64el 20241118.git6e4e94b0-0ubuntu1 [537 MB] 142s Fetched 538 MB in 50s (10.9 MB/s) 142s Selecting previously unselected package liblsof0. 142s (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 ... 73817 files and directories currently installed.) 142s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_ppc64el.deb ... 142s Unpacking liblsof0 (4.99.3+dfsg-2) ... 142s Preparing to unpack .../lsof_4.99.3+dfsg-2_ppc64el.deb ... 142s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 142s Preparing to unpack .../linux-firmware_20241118.git6e4e94b0-0ubuntu1_ppc64el.deb ... 142s Unpacking linux-firmware (20241118.git6e4e94b0-0ubuntu1) over (20241108.git3bbb13a7-0ubuntu1) ... 146s Setting up linux-firmware (20241118.git6e4e94b0-0ubuntu1) ... 146s Setting up liblsof0 (4.99.3+dfsg-2) ... 146s Setting up lsof (4.99.3+dfsg-2) ... 146s Processing triggers for man-db (2.13.0-1) ... 148s Processing triggers for libc-bin (2.40-1ubuntu3) ... 148s Processing triggers for initramfs-tools (0.142ubuntu35) ... 148s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 148s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 156s Reading package lists... 157s Building dependency tree... 157s Reading state information... 157s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 157s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 158s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 158s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 158s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 159s Reading package lists... 159s Reading package lists... 159s Building dependency tree... 159s Reading state information... 160s Calculating upgrade... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 160s Reading package lists... 160s Building dependency tree... 160s Reading state information... 160s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 161s autopkgtest [23:26:36]: rebooting testbed after setup commands that affected boot 165s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 196s autopkgtest [23:27:11]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 199s autopkgtest [23:27:14]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 204s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B] 204s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB] 204s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB] 204s gpgv: Signature made Mon May 27 20:43:46 2024 UTC 204s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 204s gpgv: issuer "emollier@debian.org" 204s gpgv: Can't check signature: No public key 204s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found 204s autopkgtest [23:27:19]: testing package python-biom-format version 2.1.16-1 205s autopkgtest [23:27:20]: build not needed 210s autopkgtest [23:27:25]: test run-unit-test: preparing testbed 212s Reading package lists... 212s Building dependency tree... 212s Reading state information... 212s Starting pkgProblemResolver with broken count: 0 212s Starting 2 pkgProblemResolver with broken count: 0 212s Done 212s The following additional packages will be installed: 212s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 212s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 212s libsz2 python-biom-format-doc python3-biom-format python3-click 212s python3-colorama python3-dateutil python3-decorator python3-h5py 212s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 212s python3-scipy python3-tz 212s Suggested packages: 212s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 212s python-pandas-doc python3-statsmodels python-scipy-doc 212s Recommended packages: 212s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 212s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 212s python3-tables g++ | c++-compiler python3-pil 212s The following NEW packages will be installed: 212s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 212s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 212s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 212s python3-click python3-colorama python3-dateutil python3-decorator 212s python3-h5py python3-h5py-serial python3-numpy python3-pandas 212s python3-pandas-lib python3-scipy python3-tz 212s 0 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. 212s Need to get 44.9 MB/44.9 MB of archives. 212s After this operation, 276 MB of additional disk space will be used. 212s Get:1 /tmp/autopkgtest.6G7beg/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 212s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 213s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 213s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 213s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 213s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB] 213s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB] 213s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 213s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 213s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB] 213s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 213s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 213s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 213s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-biom-format-doc all 2.1.16-1 [57.5 kB] 213s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 214s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-h5py-serial ppc64el 3.11.0-8ubuntu1 [1597 kB] 214s Get:17 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-h5py all 3.11.0-8ubuntu1 [7982 B] 214s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 214s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-click all 8.1.7-2 [79.5 kB] 214s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 214s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 214s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5ubuntu1 [7350 kB] 214s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 214s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 214s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5ubuntu1 [21.5 MB] 215s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biom-format ppc64el 2.1.16-1 [152 kB] 215s Fetched 44.9 MB in 3s (17.6 MB/s) 215s Selecting previously unselected package libaec0:ppc64el. 216s (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 ... 73847 files and directories currently installed.) 216s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 216s Unpacking libaec0:ppc64el (1.1.3-1) ... 216s Selecting previously unselected package libblas3:ppc64el. 216s Preparing to unpack .../01-libblas3_3.12.0-3build2_ppc64el.deb ... 216s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 216s Selecting previously unselected package libgfortran5:ppc64el. 216s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 216s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 216s Selecting previously unselected package libsz2:ppc64el. 216s Preparing to unpack .../03-libsz2_1.1.3-1_ppc64el.deb ... 216s Unpacking libsz2:ppc64el (1.1.3-1) ... 216s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 216s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 216s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 216s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 216s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 216s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 216s Selecting previously unselected package libjs-jquery. 216s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 216s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 216s Selecting previously unselected package libjs-underscore. 216s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 216s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 216s Selecting previously unselected package libjs-sphinxdoc. 216s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 216s Unpacking libjs-sphinxdoc (7.4.7-4) ... 216s Selecting previously unselected package liblapack3:ppc64el. 216s Preparing to unpack .../09-liblapack3_3.12.0-3build2_ppc64el.deb ... 216s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 216s Selecting previously unselected package liblbfgsb0:ppc64el. 216s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 216s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 216s Selecting previously unselected package liblzf1:ppc64el. 216s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ... 216s Unpacking liblzf1:ppc64el (3.6-4) ... 216s Selecting previously unselected package python-biom-format-doc. 216s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ... 216s Unpacking python-biom-format-doc (2.1.16-1) ... 216s Selecting previously unselected package python3-numpy. 216s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 216s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 216s Selecting previously unselected package python3-h5py-serial. 216s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu1_ppc64el.deb ... 216s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 216s Selecting previously unselected package python3-h5py. 216s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu1_all.deb ... 216s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 216s Selecting previously unselected package python3-colorama. 216s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 216s Unpacking python3-colorama (0.4.6-4) ... 216s Selecting previously unselected package python3-click. 216s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 216s Unpacking python3-click (8.1.7-2) ... 216s Selecting previously unselected package python3-dateutil. 216s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 216s Unpacking python3-dateutil (2.9.0-3) ... 216s Selecting previously unselected package python3-tz. 216s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 216s Unpacking python3-tz (2024.1-2) ... 216s Selecting previously unselected package python3-pandas-lib:ppc64el. 216s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_ppc64el.deb ... 216s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 216s Selecting previously unselected package python3-pandas. 216s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 216s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 217s Selecting previously unselected package python3-decorator. 217s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 217s Unpacking python3-decorator (5.1.1-5) ... 217s Selecting previously unselected package python3-scipy. 217s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_ppc64el.deb ... 217s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 217s Selecting previously unselected package python3-biom-format. 217s Preparing to unpack .../24-python3-biom-format_2.1.16-1_ppc64el.deb ... 217s Unpacking python3-biom-format (2.1.16-1) ... 218s Selecting previously unselected package autopkgtest-satdep. 218s Preparing to unpack .../25-1-autopkgtest-satdep.deb ... 218s Unpacking autopkgtest-satdep (0) ... 218s Setting up python3-colorama (0.4.6-4) ... 218s Setting up python3-click (8.1.7-2) ... 218s Setting up libaec0:ppc64el (1.1.3-1) ... 218s Setting up python3-tz (2024.1-2) ... 218s Setting up python3-decorator (5.1.1-5) ... 218s Setting up libblas3:ppc64el (3.12.0-3build2) ... 218s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 218s Setting up liblzf1:ppc64el (3.6-4) ... 218s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 218s Setting up python3-dateutil (2.9.0-3) ... 218s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 218s Setting up libsz2:ppc64el (1.1.3-1) ... 218s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 218s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 218s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 218s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 220s Setting up libjs-sphinxdoc (7.4.7-4) ... 220s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 220s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 220s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 220s Setting up python3-scipy (1.13.1-5ubuntu1) ... 225s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 225s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 225s Setting up python-biom-format-doc (2.1.16-1) ... 225s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 231s Setting up python3-h5py (3.11.0-8ubuntu1) ... 231s Setting up python3-biom-format (2.1.16-1) ... 231s Setting up autopkgtest-satdep (0) ... 231s Processing triggers for man-db (2.13.0-1) ... 233s Processing triggers for libc-bin (2.40-1ubuntu3) ... 235s (Reading database ... 78558 files and directories currently installed.) 235s Removing autopkgtest-satdep (0) ... 236s autopkgtest [23:27:51]: test run-unit-test: [----------------------- 237s 237s System information 237s ================== 237s Platform: linux 237s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 237s Python executable: /usr/bin/python3 237s 237s Dependency versions 237s =================== 237s click version: 8.1.7 237s NumPy version: 1.26.4 237s SciPy version: 1.13.1 237s h5py version: 3.11.0 237s 237s biom-format package information 237s =============================== 237s biom-format version: 2.1.16 237s 238s 238s The input file is a valid BIOM-formatted file. 239s 239s The input file is a valid BIOM-formatted file. 240s 240s The input file is a valid BIOM-formatted file. 241s 241s The input file is a valid BIOM-formatted file. 242s + table=examples/min_sparse_otu_table_hdf5.biom 242s + obsmd=examples/obs_md.txt 242s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 242s + biom show-install-info 243s 243s System information 243s ================== 243s Platform: linux 243s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 243s Python executable: /usr/bin/python3 243s 243s Dependency versions 243s =================== 243s click version: 8.1.7 243s NumPy version: 1.26.4 243s SciPy version: 1.13.1 243s h5py version: 3.11.0 243s 243s biom-format package information 243s =============================== 243s biom-format version: 2.1.16 243s 243s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 244s 244s The input file is a valid BIOM-formatted file. 244s + 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 245s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 246s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 246s + biom validate-table -i test_json.biom 247s 247s The input file is a valid BIOM-formatted file. 247s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 248s + biom validate-table -i test_hdf5.biom 249s 249s The input file is a valid BIOM-formatted file. 249s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 250s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 250s + biom validate-table -i test_hdf5.biom 251s 251s The input file is a valid BIOM-formatted file. 251s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 252s + biom validate-table -i test_json.biom 253s 253s The input file is a valid BIOM-formatted file. 253s + biom head -i examples/min_sparse_otu_table_hdf5.biom 254s # Constructed from biom file 254s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 254s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 254s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 254s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 254s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 254s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 254s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 254s Sample1 254s Sample2 254s Sample3 254s Sample4 254s Sample5 254s Sample6 254s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 255s + cat 255s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 256s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 257s Num samples: 6 257s Num observations: 5 257s Total count: 27 257s Table density (fraction of non-zero values): 0.500 257s 257s Counts/sample summary: 257s Min: 3.000 257s Max: 7.000 257s Median: 4.000 257s Mean: 4.500 257s Std. dev.: 1.500 257s Sample Metadata Categories: None provided 257s Observation Metadata Categories: None provided 257s 257s Counts/sample detail: 257s Sample2: 3.000 257s Sample5: 3.000 257s Sample3: 4.000 257s Sample6: 4.000 257s Sample4: 6.000 257s Sample1: 7.000 257s + cat 257s + biom from-uc -i uctest -o test_uc.biom 258s If this message was shown, then all commands executed without failure 258s + echo If this message was shown, then all commands executed without failure 258s autopkgtest [23:28:13]: test run-unit-test: -----------------------] 258s run-unit-test PASS 258s autopkgtest [23:28:13]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 259s autopkgtest [23:28:14]: test autodep8-python3: preparing testbed 414s autopkgtest [23:30:49]: testbed dpkg architecture: ppc64el 414s autopkgtest [23:30:49]: testbed apt version: 2.9.8 414s autopkgtest [23:30:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 415s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 415s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 416s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [72.1 kB] 416s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.5 kB] 416s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [817 kB] 416s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [87.5 kB] 416s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [621 kB] 416s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [6788 B] 416s Fetched 1699 kB in 1s (1668 kB/s) 416s Reading package lists... 418s Reading package lists... 419s Building dependency tree... 419s Reading state information... 419s Calculating upgrade... 419s The following NEW packages will be installed: 419s liblsof0 419s The following packages will be upgraded: 419s linux-firmware lsof 419s 2 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 419s Need to get 538 MB of archives. 419s After this operation, 1614 kB of additional disk space will be used. 419s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsof0 ppc64el 4.99.3+dfsg-2 [68.1 kB] 419s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el lsof ppc64el 4.99.3+dfsg-2 [255 kB] 420s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el linux-firmware ppc64el 20241118.git6e4e94b0-0ubuntu1 [537 MB] 441s Fetched 538 MB in 22s (24.3 MB/s) 442s Selecting previously unselected package liblsof0. 442s (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 ... 73817 files and directories currently installed.) 442s Preparing to unpack .../liblsof0_4.99.3+dfsg-2_ppc64el.deb ... 442s Unpacking liblsof0 (4.99.3+dfsg-2) ... 442s Preparing to unpack .../lsof_4.99.3+dfsg-2_ppc64el.deb ... 442s Unpacking lsof (4.99.3+dfsg-2) over (4.95.0-1.1) ... 442s Preparing to unpack .../linux-firmware_20241118.git6e4e94b0-0ubuntu1_ppc64el.deb ... 442s Unpacking linux-firmware (20241118.git6e4e94b0-0ubuntu1) over (20241108.git3bbb13a7-0ubuntu1) ... 445s Setting up linux-firmware (20241118.git6e4e94b0-0ubuntu1) ... 445s Setting up liblsof0 (4.99.3+dfsg-2) ... 445s Setting up lsof (4.99.3+dfsg-2) ... 445s Processing triggers for man-db (2.13.0-1) ... 446s Processing triggers for libc-bin (2.40-1ubuntu3) ... 446s Processing triggers for initramfs-tools (0.142ubuntu35) ... 446s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 446s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 455s Reading package lists... 455s Building dependency tree... 455s Reading state information... 455s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 455s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 455s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 456s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 456s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 457s Reading package lists... 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 457s Calculating upgrade... 457s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 457s Reading package lists... 457s Building dependency tree... 457s Reading state information... 458s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 458s autopkgtest [23:31:33]: rebooting testbed after setup commands that affected boot 493s Reading package lists... 494s Building dependency tree... 494s Reading state information... 494s Starting pkgProblemResolver with broken count: 0 494s Starting 2 pkgProblemResolver with broken count: 0 494s Done 494s The following additional packages will be installed: 494s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 494s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 494s python3-colorama python3-dateutil python3-decorator python3-h5py 494s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 494s python3-scipy python3-tz 494s Suggested packages: 494s python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc 494s python3-dev python3-pytest python-pandas-doc python3-statsmodels 494s python-scipy-doc 494s Recommended packages: 494s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 494s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 494s g++ | c++-compiler python3-pil 494s The following NEW packages will be installed: 494s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 494s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all 494s python3-biom-format python3-click python3-colorama python3-dateutil 494s python3-decorator python3-h5py python3-h5py-serial python3-numpy 494s python3-pandas python3-pandas-lib python3-scipy python3-tz 494s 0 upgraded, 23 newly installed, 0 to remove and 0 not upgraded. 494s Need to get 44.2 MB/44.2 MB of archives. 494s After this operation, 274 MB of additional disk space will be used. 494s Get:1 /tmp/autopkgtest.6G7beg/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 494s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 495s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB] 495s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB] 495s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 495s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB] 495s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB] 495s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB] 495s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 495s Get:10 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 495s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B] 495s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB] 495s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-h5py-serial ppc64el 3.11.0-8ubuntu1 [1597 kB] 495s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el python3-h5py all 3.11.0-8ubuntu1 [7982 B] 495s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 495s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-click all 8.1.7-2 [79.5 kB] 495s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-3 [80.2 kB] 495s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB] 495s Get:19 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5ubuntu1 [7350 kB] 496s Get:20 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 496s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 496s Get:22 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5ubuntu1 [21.5 MB] 496s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biom-format ppc64el 2.1.16-1 [152 kB] 497s Fetched 44.2 MB in 2s (20.6 MB/s) 497s Selecting previously unselected package libaec0:ppc64el. 497s (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 ... 73847 files and directories currently installed.) 497s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 497s Unpacking libaec0:ppc64el (1.1.3-1) ... 497s Selecting previously unselected package libblas3:ppc64el. 497s Preparing to unpack .../01-libblas3_3.12.0-3build2_ppc64el.deb ... 497s Unpacking libblas3:ppc64el (3.12.0-3build2) ... 497s Selecting previously unselected package libgfortran5:ppc64el. 497s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ... 497s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 497s Selecting previously unselected package libsz2:ppc64el. 497s Preparing to unpack .../03-libsz2_1.1.3-1_ppc64el.deb ... 497s Unpacking libsz2:ppc64el (1.1.3-1) ... 497s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 497s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 497s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 497s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 497s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ... 497s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 497s Selecting previously unselected package liblapack3:ppc64el. 497s Preparing to unpack .../06-liblapack3_3.12.0-3build2_ppc64el.deb ... 497s Unpacking liblapack3:ppc64el (3.12.0-3build2) ... 498s Selecting previously unselected package liblbfgsb0:ppc64el. 498s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 498s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 498s Selecting previously unselected package liblzf1:ppc64el. 498s Preparing to unpack .../08-liblzf1_3.6-4_ppc64el.deb ... 498s Unpacking liblzf1:ppc64el (3.6-4) ... 498s Selecting previously unselected package python3-all. 498s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_ppc64el.deb ... 498s Unpacking python3-all (3.12.6-0ubuntu1) ... 498s Selecting previously unselected package python3-numpy. 498s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ... 498s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 498s Selecting previously unselected package python3-h5py-serial. 498s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu1_ppc64el.deb ... 498s Unpacking python3-h5py-serial (3.11.0-8ubuntu1) ... 498s Selecting previously unselected package python3-h5py. 498s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu1_all.deb ... 498s Unpacking python3-h5py (3.11.0-8ubuntu1) ... 498s Selecting previously unselected package python3-colorama. 498s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 498s Unpacking python3-colorama (0.4.6-4) ... 498s Selecting previously unselected package python3-click. 498s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 498s Unpacking python3-click (8.1.7-2) ... 498s Selecting previously unselected package python3-dateutil. 498s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 498s Unpacking python3-dateutil (2.9.0-3) ... 498s Selecting previously unselected package python3-tz. 498s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 498s Unpacking python3-tz (2024.1-2) ... 498s Selecting previously unselected package python3-pandas-lib:ppc64el. 498s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_ppc64el.deb ... 498s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 498s Selecting previously unselected package python3-pandas. 498s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 498s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 499s Selecting previously unselected package python3-decorator. 499s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 499s Unpacking python3-decorator (5.1.1-5) ... 499s Selecting previously unselected package python3-scipy. 499s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_ppc64el.deb ... 499s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 499s Selecting previously unselected package python3-biom-format. 499s Preparing to unpack .../21-python3-biom-format_2.1.16-1_ppc64el.deb ... 499s Unpacking python3-biom-format (2.1.16-1) ... 499s Selecting previously unselected package autopkgtest-satdep. 499s Preparing to unpack .../22-2-autopkgtest-satdep.deb ... 499s Unpacking autopkgtest-satdep (0) ... 499s Setting up python3-colorama (0.4.6-4) ... 500s Setting up python3-all (3.12.6-0ubuntu1) ... 500s Setting up python3-click (8.1.7-2) ... 500s Setting up libaec0:ppc64el (1.1.3-1) ... 500s Setting up python3-tz (2024.1-2) ... 500s Setting up python3-decorator (5.1.1-5) ... 500s Setting up libblas3:ppc64el (3.12.0-3build2) ... 500s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 500s Setting up liblzf1:ppc64el (3.6-4) ... 500s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ... 500s Setting up python3-dateutil (2.9.0-3) ... 500s Setting up libsz2:ppc64el (1.1.3-1) ... 500s Setting up liblapack3:ppc64el (3.12.0-3build2) ... 500s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 500s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 502s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ... 502s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 502s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ... 502s Setting up python3-scipy (1.13.1-5ubuntu1) ... 506s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5ubuntu1) ... 506s Setting up python3-h5py-serial (3.11.0-8ubuntu1) ... 507s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 513s Setting up python3-h5py (3.11.0-8ubuntu1) ... 513s Setting up python3-biom-format (2.1.16-1) ... 513s Setting up autopkgtest-satdep (0) ... 513s Processing triggers for man-db (2.13.0-1) ... 514s Processing triggers for libc-bin (2.40-1ubuntu3) ... 517s (Reading database ... 78460 files and directories currently installed.) 517s Removing autopkgtest-satdep (0) ... 521s autopkgtest [23:32:36]: 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 521s autopkgtest [23:32:36]: test autodep8-python3: [----------------------- 521s Testing with python3.12: 522s 523s autopkgtest [23:32:38]: test autodep8-python3: -----------------------] 523s autopkgtest [23:32:38]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 523s autodep8-python3 PASS (superficial) 523s autopkgtest [23:32:38]: @@@@@@@@@@@@@@@@@@@@ summary 523s run-unit-test PASS 523s autodep8-python3 PASS (superficial) 528s nova [W] Using flock in prodstack6-ppc64el 528s Creating nova instance adt-plucky-ppc64el-python-biom-format-20241118-232355-juju-7f2275-prod-proposed-migration-environment-20-e5401589-ecf1-433f-bce0-7be4c70ace98 from image adt/ubuntu-plucky-ppc64el-server-20241118.img (UUID 6881a927-1825-44a5-92f2-5f029c9bf803)... 528s nova [W] Using flock in prodstack6-ppc64el 528s Creating nova instance adt-plucky-ppc64el-python-biom-format-20241118-232355-juju-7f2275-prod-proposed-migration-environment-20-e5401589-ecf1-433f-bce0-7be4c70ace98 from image adt/ubuntu-plucky-ppc64el-server-20241118.img (UUID 6881a927-1825-44a5-92f2-5f029c9bf803)...