0s autopkgtest [02:04:51]: starting date and time: 2024-03-23 02:04:51+0000 0s autopkgtest [02:04:51]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [02:04:51]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.us_ixv1r/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-12.secgroup --name adt-noble-ppc64el-python-biom-format-20240323-020450-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 93s autopkgtest [02:06:24]: testbed dpkg architecture: ppc64el 93s autopkgtest [02:06:24]: testbed apt version: 2.7.12 93s autopkgtest [02:06:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup 94s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 94s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 94s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 94s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4035 kB] 95s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 95s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [668 kB] 95s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 95s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 95s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 95s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4263 kB] 95s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 95s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.5 kB] 95s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 98s Fetched 9718 kB in 3s (3799 kB/s) 98s Reading package lists... 101s Reading package lists... 102s Building dependency tree... 102s Reading state information... 102s Calculating upgrade... 102s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 102s Reading package lists... 102s Building dependency tree... 102s Reading state information... 103s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 103s sh: Attempting to set up Debian/Ubuntu apt sources automatically 103s sh: Distribution appears to be Ubuntu 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s eatmydata is already the newest version (131-1). 104s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s dbus is already the newest version (1.14.10-4ubuntu1). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 105s rng-tools-debian is already the newest version (2.4). 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s The following packages will be REMOVED: 106s cloud-init* python3-configobj* python3-debconf* 106s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 106s After this operation, 3256 kB disk space will be freed. 106s (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 ... 70156 files and directories currently installed.) 106s Removing cloud-init (24.1.2-0ubuntu1) ... 106s Removing python3-configobj (5.0.8-3) ... 107s Removing python3-debconf (1.5.86) ... 107s Processing triggers for man-db (2.12.0-3) ... 107s (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 ... 69767 files and directories currently installed.) 107s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 108s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 108s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 108s invoke-rc.d: policy-rc.d denied execution of try-restart. 108s Reading package lists... 108s Building dependency tree... 108s Reading state information... 108s linux-generic is already the newest version (6.8.0-11.11+1). 108s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 111s Reading package lists... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s Calculating upgrade... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 112s autopkgtest [02:06:43]: rebooting testbed after setup commands that affected boot 148s autopkgtest [02:07:19]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 150s autopkgtest [02:07:21]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 154s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (dsc) [1883 B] 154s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (tar) [11.9 MB] 154s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-biom-format 2.1.15.2-3 (diff) [11.5 kB] 154s gpgv: Signature made Sun Feb 4 19:23:04 2024 UTC 154s gpgv: using EDDSA key A095B66EE09024BEE6A2F0722A27904BD7243EDA 154s gpgv: Can't check signature: No public key 154s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.15.2-3.dsc: no acceptable signature found 155s autopkgtest [02:07:26]: testing package python-biom-format version 2.1.15.2-3 155s autopkgtest [02:07:26]: build not needed 161s autopkgtest [02:07:32]: test run-unit-test: preparing testbed 164s Reading package lists... 164s Building dependency tree... 164s Reading state information... 164s Starting pkgProblemResolver with broken count: 0 164s Starting 2 pkgProblemResolver with broken count: 0 164s Done 165s The following additional packages will be installed: 165s libaec0 libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 libjs-jquery 165s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 165s python-biom-format-doc python3-biom-format python3-click python3-colorama 165s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 165s python3-numpy python3-pandas python3-pandas-lib python3-scipy 165s Suggested packages: 165s python-h5py-doc gcc gfortran python3-dev python3-pytest python-pandas-doc 165s python3-statsmodels python-scipy-doc 165s Recommended packages: 165s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 165s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 165s python3-tables g++ | c++-compiler python3-pil 165s The following NEW packages will be installed: 165s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1 165s libhdf5-hl-100 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 165s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 165s python3-click python3-colorama python3-dateutil python3-decorator 165s python3-h5py python3-h5py-serial python3-numpy python3-pandas 165s python3-pandas-lib python3-scipy 165s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 165s Need to get 46.7 MB/46.7 MB of archives. 165s After this operation, 263 MB of additional disk space will be used. 165s Get:1 /tmp/autopkgtest.gekLS7/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 165s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 165s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 165s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 165s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 165s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 165s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 165s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 165s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 165s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el libjs-sphinxdoc all 7.2.6-4 [149 kB] 165s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 166s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 166s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 166s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el python-biom-format-doc all 2.1.15.2-3 [57.1 kB] 166s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 166s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 166s Get:17 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 166s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 166s Get:19 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-click all 8.1.6-1 [79.0 kB] 166s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 166s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 166s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 166s Get:23 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 166s Get:24 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 167s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biom-format ppc64el 2.1.15.2-3 [195 kB] 167s Fetched 46.7 MB in 2s (19.1 MB/s) 167s Selecting previously unselected package libaec0:ppc64el. 167s (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 ... 69712 files and directories currently installed.) 167s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 167s Unpacking libaec0:ppc64el (1.1.2-1) ... 167s Selecting previously unselected package libblas3:ppc64el. 167s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 167s Unpacking libblas3:ppc64el (3.12.0-3) ... 167s Selecting previously unselected package libgfortran5:ppc64el. 167s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 167s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 167s Selecting previously unselected package libsz2:ppc64el. 167s Preparing to unpack .../03-libsz2_1.1.2-1_ppc64el.deb ... 167s Unpacking libsz2:ppc64el (1.1.2-1) ... 168s Selecting previously unselected package libhdf5-103-1:ppc64el. 168s Preparing to unpack .../04-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 168s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 168s Selecting previously unselected package libhdf5-hl-100:ppc64el. 168s Preparing to unpack .../05-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 168s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 168s Selecting previously unselected package libjs-jquery. 168s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 168s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 168s Selecting previously unselected package libjs-underscore. 168s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 168s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 168s Selecting previously unselected package libjs-sphinxdoc. 168s Preparing to unpack .../08-libjs-sphinxdoc_7.2.6-4_all.deb ... 168s Unpacking libjs-sphinxdoc (7.2.6-4) ... 168s Selecting previously unselected package liblapack3:ppc64el. 168s Preparing to unpack .../09-liblapack3_3.12.0-3_ppc64el.deb ... 168s Unpacking liblapack3:ppc64el (3.12.0-3) ... 168s Selecting previously unselected package liblbfgsb0:ppc64el. 168s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 168s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 168s Selecting previously unselected package liblzf1:ppc64el. 168s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ... 168s Unpacking liblzf1:ppc64el (3.6-4) ... 168s Selecting previously unselected package python-biom-format-doc. 168s Preparing to unpack .../12-python-biom-format-doc_2.1.15.2-3_all.deb ... 168s Unpacking python-biom-format-doc (2.1.15.2-3) ... 168s Selecting previously unselected package python3-numpy. 168s Preparing to unpack .../13-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 168s Unpacking python3-numpy (1:1.24.2-2) ... 168s Selecting previously unselected package python3-h5py-serial. 168s Preparing to unpack .../14-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 168s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 168s Selecting previously unselected package python3-h5py. 168s Preparing to unpack .../15-python3-h5py_3.10.0-1ubuntu1_all.deb ... 168s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 168s Selecting previously unselected package python3-colorama. 168s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 168s Unpacking python3-colorama (0.4.6-4) ... 168s Selecting previously unselected package python3-click. 168s Preparing to unpack .../17-python3-click_8.1.6-1_all.deb ... 168s Unpacking python3-click (8.1.6-1) ... 168s Selecting previously unselected package python3-dateutil. 168s Preparing to unpack .../18-python3-dateutil_2.8.2-3_all.deb ... 168s Unpacking python3-dateutil (2.8.2-3) ... 168s Selecting previously unselected package python3-pandas-lib:ppc64el. 168s Preparing to unpack .../19-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 168s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 169s Selecting previously unselected package python3-pandas. 169s Preparing to unpack .../20-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 169s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 169s Selecting previously unselected package python3-decorator. 169s Preparing to unpack .../21-python3-decorator_5.1.1-5_all.deb ... 169s Unpacking python3-decorator (5.1.1-5) ... 169s Selecting previously unselected package python3-scipy. 169s Preparing to unpack .../22-python3-scipy_1.11.4-6_ppc64el.deb ... 169s Unpacking python3-scipy (1.11.4-6) ... 170s Selecting previously unselected package python3-biom-format. 170s Preparing to unpack .../23-python3-biom-format_2.1.15.2-3_ppc64el.deb ... 170s Unpacking python3-biom-format (2.1.15.2-3) ... 170s Selecting previously unselected package autopkgtest-satdep. 170s Preparing to unpack .../24-1-autopkgtest-satdep.deb ... 170s Unpacking autopkgtest-satdep (0) ... 170s Setting up python3-colorama (0.4.6-4) ... 170s Setting up python3-click (8.1.6-1) ... 170s Setting up libaec0:ppc64el (1.1.2-1) ... 170s Setting up python3-decorator (5.1.1-5) ... 170s Setting up libblas3:ppc64el (3.12.0-3) ... 170s 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 170s Setting up liblzf1:ppc64el (3.6-4) ... 170s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 170s Setting up python3-dateutil (2.8.2-3) ... 171s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 171s Setting up libsz2:ppc64el (1.1.2-1) ... 171s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 171s Setting up liblapack3:ppc64el (3.12.0-3) ... 171s 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 171s Setting up python3-numpy (1:1.24.2-2) ... 173s Setting up libjs-sphinxdoc (7.2.6-4) ... 173s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 173s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 173s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 173s Setting up python3-scipy (1.11.4-6) ... 176s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 176s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 176s Setting up python-biom-format-doc (2.1.15.2-3) ... 176s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 181s Setting up python3-h5py (3.10.0-1ubuntu1) ... 181s Setting up python3-biom-format (2.1.15.2-3) ... 181s Setting up autopkgtest-satdep (0) ... 181s Processing triggers for man-db (2.12.0-3) ... 182s Processing triggers for libc-bin (2.39-0ubuntu2) ... 184s (Reading database ... 74400 files and directories currently installed.) 184s Removing autopkgtest-satdep (0) ... 185s autopkgtest [02:07:56]: test run-unit-test: [----------------------- 186s 186s System information 186s ================== 186s Platform: linux 186s Python version: 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 186s Python executable: /usr/bin/python3 186s 186s Dependency versions 186s =================== 186s click version: 8.1.6 186s NumPy version: 1.24.2 186s SciPy version: 1.11.4 186s h5py version: 3.10.0 186s 186s biom-format package information 186s =============================== 186s biom-format version: 2.1.15 186s 187s 187s The input file is a valid BIOM-formatted file. 187s 187s The input file is a valid BIOM-formatted file. 188s 188s The input file is a valid BIOM-formatted file. 189s 189s The input file is a valid BIOM-formatted file. 191s + table=examples/min_sparse_otu_table_hdf5.biom 191s + obsmd=examples/obs_md.txt 191s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 191s + biom show-install-info 191s 191s System information 191s ================== 191s Platform: linux 191s Python version: 3.12.2 (main, Feb 7 2024, 20:47:03) [GCC 13.2.0] 191s Python executable: /usr/bin/python3 191s 191s Dependency versions 191s =================== 191s click version: 8.1.6 191s NumPy version: 1.24.2 191s SciPy version: 1.11.4 191s h5py version: 3.10.0 191s 191s biom-format package information 191s =============================== 191s biom-format version: 2.1.15 191s 191s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 192s 192s The input file is a valid BIOM-formatted file. 192s + 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 193s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 194s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 194s + biom validate-table -i test_json.biom 195s 195s The input file is a valid BIOM-formatted file. 195s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 196s + biom validate-table -i test_hdf5.biom 196s 196s The input file is a valid BIOM-formatted file. 196s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 197s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 198s + biom validate-table -i test_hdf5.biom 199s 199s The input file is a valid BIOM-formatted file. 199s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 199s + biom validate-table -i test_json.biom 200s 200s The input file is a valid BIOM-formatted file. 200s + biom head -i examples/min_sparse_otu_table_hdf5.biom 201s # Constructed from biom file 201s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 201s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 201s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 201s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 201s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 201s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 201s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 202s Sample1 202s Sample2 202s Sample3 202s Sample4 202s Sample5 202s Sample6 202s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 202s + cat 202s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 203s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 204s Num samples: 6 204s Num observations: 5 204s Total count: 27 204s Table density (fraction of non-zero values): 0.500 204s 204s Counts/sample summary: 204s Min: 3.000 204s Max: 7.000 204s Median: 4.000 204s Mean: 4.500 204s Std. dev.: 1.500 204s Sample Metadata Categories: None provided 204s Observation Metadata Categories: None provided 204s 204s Counts/sample detail: 204s Sample2: 3.000 204s Sample5: 3.000 204s Sample3: 4.000 204s Sample6: 4.000 204s Sample4: 6.000 204s Sample1: 7.000 204s + cat 204s + biom from-uc -i uctest -o test_uc.biom 205s If this message was shown, then all commands executed without failure 205s + echo If this message was shown, then all commands executed without failure 205s autopkgtest [02:08:16]: test run-unit-test: -----------------------] 206s autopkgtest [02:08:17]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 206s run-unit-test PASS 206s autopkgtest [02:08:17]: test autodep8-python3: preparing testbed 311s autopkgtest [02:10:02]: testbed dpkg architecture: ppc64el 311s autopkgtest [02:10:02]: testbed apt version: 2.7.12 311s autopkgtest [02:10:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 312s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 312s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4035 kB] 313s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 313s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 313s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.7 kB] 313s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [668 kB] 313s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 313s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 313s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 313s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4263 kB] 314s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 314s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [61.5 kB] 314s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 317s Fetched 9718 kB in 3s (3534 kB/s) 317s Reading package lists... 319s Reading package lists... 319s Building dependency tree... 319s Reading state information... 320s Calculating upgrade... 320s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 320s Reading package lists... 320s Building dependency tree... 320s Reading state information... 320s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 321s sh: Attempting to set up Debian/Ubuntu apt sources automatically 321s sh: Distribution appears to be Ubuntu 322s Reading package lists... 322s Building dependency tree... 322s Reading state information... 322s eatmydata is already the newest version (131-1). 322s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 322s Reading package lists... 322s Building dependency tree... 322s Reading state information... 322s dbus is already the newest version (1.14.10-4ubuntu1). 322s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 322s Reading package lists... 322s Building dependency tree... 322s Reading state information... 323s rng-tools-debian is already the newest version (2.4). 323s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 323s Reading package lists... 323s Building dependency tree... 323s Reading state information... 323s The following packages will be REMOVED: 323s cloud-init* python3-configobj* python3-debconf* 323s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 323s After this operation, 3256 kB disk space will be freed. 323s (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 ... 70156 files and directories currently installed.) 323s Removing cloud-init (24.1.2-0ubuntu1) ... 324s Removing python3-configobj (5.0.8-3) ... 324s Removing python3-debconf (1.5.86) ... 324s Processing triggers for man-db (2.12.0-3) ... 324s (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 ... 69767 files and directories currently installed.) 324s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 325s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 325s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 325s invoke-rc.d: policy-rc.d denied execution of try-restart. 325s Reading package lists... 325s Building dependency tree... 325s Reading state information... 325s linux-generic is already the newest version (6.8.0-11.11+1). 325s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 326s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 326s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 326s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 328s Reading package lists... 328s Reading package lists... 328s Building dependency tree... 328s Reading state information... 329s Calculating upgrade... 329s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 329s Reading package lists... 329s Building dependency tree... 329s Reading state information... 329s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 329s autopkgtest [02:10:20]: rebooting testbed after setup commands that affected boot 373s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 385s Reading package lists... 386s Building dependency tree... 386s Reading state information... 386s Starting pkgProblemResolver with broken count: 0 386s Starting 2 pkgProblemResolver with broken count: 0 386s Done 386s The following additional packages will be installed: 386s libaec0 libblas3 libgfortran5 libhdf5-103-1 libhdf5-hl-100 liblapack3 386s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 386s python3-colorama python3-dateutil python3-decorator python3-h5py 386s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 386s python3-scipy 386s Suggested packages: 386s python-biom-format-doc python-h5py-doc gcc gfortran python3-dev 386s python3-pytest python-pandas-doc python3-statsmodels python-scipy-doc 386s Recommended packages: 386s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 386s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 386s g++ | c++-compiler python3-pil 386s The following NEW packages will be installed: 386s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1 386s libhdf5-hl-100 liblapack3 liblbfgsb0 liblzf1 libsz2 python3-all 386s python3-biom-format python3-click python3-colorama python3-dateutil 386s python3-decorator python3-h5py python3-h5py-serial python3-numpy 386s python3-pandas python3-pandas-lib python3-scipy 386s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 386s Need to get 46.1 MB/46.1 MB of archives. 386s After this operation, 261 MB of additional disk space will be used. 386s Get:1 /tmp/autopkgtest.gekLS7/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B] 386s Get:2 http://ftpmaster.internal/ubuntu noble/universe ppc64el libaec0 ppc64el 1.1.2-1 [29.9 kB] 386s Get:3 http://ftpmaster.internal/ubuntu noble/main ppc64el libblas3 ppc64el 3.12.0-3 [227 kB] 387s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libgfortran5 ppc64el 14-20240303-1ubuntu1 [574 kB] 387s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libsz2 ppc64el 1.1.2-1 [5472 B] 387s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-103-1 ppc64el 1.10.10+repack-3ubuntu1 [1375 kB] 387s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhdf5-hl-100 ppc64el 1.10.10+repack-3ubuntu1 [69.9 kB] 387s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el liblapack3 ppc64el 3.12.0-3 [2804 kB] 388s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1 [32.8 kB] 388s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 388s Get:11 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-all ppc64el 3.12.1-0ubuntu2 [904 B] 388s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-numpy ppc64el 1:1.24.2-2 [5581 kB] 389s Get:13 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu1 [1635 kB] 390s Get:14 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-h5py all 3.10.0-1ubuntu1 [7970 B] 390s Get:15 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 390s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-click all 8.1.6-1 [79.0 kB] 390s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-dateutil all 2.8.2-3 [79.2 kB] 390s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas-lib ppc64el 2.1.4+dfsg-4ubuntu2 [8837 kB] 393s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 394s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 394s Get:21 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-scipy ppc64el 1.11.4-6 [21.4 MB] 402s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el python3-biom-format ppc64el 2.1.15.2-3 [195 kB] 402s Fetched 46.1 MB in 16s (2901 kB/s) 402s Selecting previously unselected package libaec0:ppc64el. 402s (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 ... 69712 files and directories currently installed.) 402s Preparing to unpack .../00-libaec0_1.1.2-1_ppc64el.deb ... 402s Unpacking libaec0:ppc64el (1.1.2-1) ... 402s Selecting previously unselected package libblas3:ppc64el. 402s Preparing to unpack .../01-libblas3_3.12.0-3_ppc64el.deb ... 402s Unpacking libblas3:ppc64el (3.12.0-3) ... 403s Selecting previously unselected package libgfortran5:ppc64el. 403s Preparing to unpack .../02-libgfortran5_14-20240303-1ubuntu1_ppc64el.deb ... 403s Unpacking libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 403s Selecting previously unselected package libsz2:ppc64el. 403s Preparing to unpack .../03-libsz2_1.1.2-1_ppc64el.deb ... 403s Unpacking libsz2:ppc64el (1.1.2-1) ... 403s Selecting previously unselected package libhdf5-103-1:ppc64el. 403s Preparing to unpack .../04-libhdf5-103-1_1.10.10+repack-3ubuntu1_ppc64el.deb ... 403s Unpacking libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 403s Selecting previously unselected package libhdf5-hl-100:ppc64el. 403s Preparing to unpack .../05-libhdf5-hl-100_1.10.10+repack-3ubuntu1_ppc64el.deb ... 403s Unpacking libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 403s Selecting previously unselected package liblapack3:ppc64el. 403s Preparing to unpack .../06-liblapack3_3.12.0-3_ppc64el.deb ... 403s Unpacking liblapack3:ppc64el (3.12.0-3) ... 403s Selecting previously unselected package liblbfgsb0:ppc64el. 403s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1_ppc64el.deb ... 403s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 403s Selecting previously unselected package liblzf1:ppc64el. 403s Preparing to unpack .../08-liblzf1_3.6-4_ppc64el.deb ... 403s Unpacking liblzf1:ppc64el (3.6-4) ... 403s Selecting previously unselected package python3-all. 403s Preparing to unpack .../09-python3-all_3.12.1-0ubuntu2_ppc64el.deb ... 403s Unpacking python3-all (3.12.1-0ubuntu2) ... 403s Selecting previously unselected package python3-numpy. 403s Preparing to unpack .../10-python3-numpy_1%3a1.24.2-2_ppc64el.deb ... 403s Unpacking python3-numpy (1:1.24.2-2) ... 403s Selecting previously unselected package python3-h5py-serial. 403s Preparing to unpack .../11-python3-h5py-serial_3.10.0-1ubuntu1_ppc64el.deb ... 403s Unpacking python3-h5py-serial (3.10.0-1ubuntu1) ... 403s Selecting previously unselected package python3-h5py. 403s Preparing to unpack .../12-python3-h5py_3.10.0-1ubuntu1_all.deb ... 403s Unpacking python3-h5py (3.10.0-1ubuntu1) ... 404s Selecting previously unselected package python3-colorama. 404s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 404s Unpacking python3-colorama (0.4.6-4) ... 404s Selecting previously unselected package python3-click. 404s Preparing to unpack .../14-python3-click_8.1.6-1_all.deb ... 404s Unpacking python3-click (8.1.6-1) ... 404s Selecting previously unselected package python3-dateutil. 404s Preparing to unpack .../15-python3-dateutil_2.8.2-3_all.deb ... 404s Unpacking python3-dateutil (2.8.2-3) ... 404s Selecting previously unselected package python3-pandas-lib:ppc64el. 404s Preparing to unpack .../16-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_ppc64el.deb ... 404s Unpacking python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 404s Selecting previously unselected package python3-pandas. 404s Preparing to unpack .../17-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 404s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 404s Selecting previously unselected package python3-decorator. 404s Preparing to unpack .../18-python3-decorator_5.1.1-5_all.deb ... 404s Unpacking python3-decorator (5.1.1-5) ... 404s Selecting previously unselected package python3-scipy. 404s Preparing to unpack .../19-python3-scipy_1.11.4-6_ppc64el.deb ... 404s Unpacking python3-scipy (1.11.4-6) ... 405s Selecting previously unselected package python3-biom-format. 405s Preparing to unpack .../20-python3-biom-format_2.1.15.2-3_ppc64el.deb ... 405s Unpacking python3-biom-format (2.1.15.2-3) ... 405s Selecting previously unselected package autopkgtest-satdep. 405s Preparing to unpack .../21-2-autopkgtest-satdep.deb ... 405s Unpacking autopkgtest-satdep (0) ... 405s Setting up python3-colorama (0.4.6-4) ... 405s Setting up python3-all (3.12.1-0ubuntu2) ... 405s Setting up python3-click (8.1.6-1) ... 405s Setting up libaec0:ppc64el (1.1.2-1) ... 405s Setting up python3-decorator (5.1.1-5) ... 406s Setting up libblas3:ppc64el (3.12.0-3) ... 406s 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 406s Setting up liblzf1:ppc64el (3.6-4) ... 406s Setting up libgfortran5:ppc64el (14-20240303-1ubuntu1) ... 406s Setting up python3-dateutil (2.8.2-3) ... 406s Setting up libsz2:ppc64el (1.1.2-1) ... 406s Setting up liblapack3:ppc64el (3.12.0-3) ... 406s 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 406s Setting up python3-numpy (1:1.24.2-2) ... 408s Setting up libhdf5-103-1:ppc64el (1.10.10+repack-3ubuntu1) ... 408s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1) ... 408s Setting up libhdf5-hl-100:ppc64el (1.10.10+repack-3ubuntu1) ... 408s Setting up python3-scipy (1.11.4-6) ... 411s Setting up python3-pandas-lib:ppc64el (2.1.4+dfsg-4ubuntu2) ... 411s Setting up python3-h5py-serial (3.10.0-1ubuntu1) ... 411s Setting up python3-pandas (2.1.4+dfsg-4ubuntu2) ... 416s Setting up python3-h5py (3.10.0-1ubuntu1) ... 416s Setting up python3-biom-format (2.1.15.2-3) ... 416s Setting up autopkgtest-satdep (0) ... 416s Processing triggers for man-db (2.12.0-3) ... 416s Processing triggers for libc-bin (2.39-0ubuntu2) ... 419s (Reading database ... 74301 files and directories currently installed.) 419s Removing autopkgtest-satdep (0) ... 428s autopkgtest [02:11:59]: 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 428s autopkgtest [02:11:59]: test autodep8-python3: [----------------------- 428s Testing with python3.12: 429s 429s autopkgtest [02:12:00]: test autodep8-python3: -----------------------] 430s autodep8-python3 PASS (superficial) 430s autopkgtest [02:12:01]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 430s autopkgtest [02:12:01]: @@@@@@@@@@@@@@@@@@@@ summary 430s run-unit-test PASS 430s autodep8-python3 PASS (superficial) 444s Creating nova instance adt-noble-ppc64el-python-biom-format-20240323-020450-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)... 444s Creating nova instance adt-noble-ppc64el-python-biom-format-20240323-020450-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240322.img (UUID 8499323f-6fcd-4f77-8a53-77410adea6d3)...