0s autopkgtest [12:32:06]: starting date and time: 2025-02-19 12:32:06+0000 0s autopkgtest [12:32:06]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [12:32:06]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2evzdf7i/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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:sphinx --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/8.1.3-5 -- lxd -r lxd-armhf-10.145.243.201 lxd-armhf-10.145.243.201:autopkgtest/ubuntu/plucky/armhf 26s autopkgtest [12:32:32]: testbed dpkg architecture: armhf 28s autopkgtest [12:32:34]: testbed apt version: 2.9.30 33s autopkgtest [12:32:39]: @@@@@@@@@@@@@@@@@@@@ test bed setup 35s autopkgtest [12:32:41]: testbed release detected to be: None 44s autopkgtest [12:32:50]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 48s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 48s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 48s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 48s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 48s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [99.0 kB] 48s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 48s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 48s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 49s Fetched 1693 kB in 2s (779 kB/s) 50s Reading package lists... 57s autopkgtest [12:33:03]: upgrading testbed (apt dist-upgrade and autopurge) 59s Reading package lists... 60s Building dependency tree... 60s Reading state information... 61s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 61s Starting 2 pkgProblemResolver with broken count: 0 61s Done 62s Entering ResolveByKeep 62s 63s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 66s Starting pkgProblemResolver with broken count: 0 66s Starting 2 pkgProblemResolver with broken count: 0 66s Done 67s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 70s autopkgtest [12:33:16]: rebooting testbed after setup commands that affected boot 117s autopkgtest [12:34:03]: testbed running kernel: Linux 6.8.0-49-generic #49~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Nov 6 18:12:14 UTC 2 146s autopkgtest [12:34:32]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 164s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (dsc) [2498 B] 164s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (tar) [11.9 MB] 164s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build2 (diff) [11.7 kB] 164s gpgv: Signature made Wed Jan 29 22:35:10 2025 UTC 164s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 164s gpgv: Can't check signature: No public key 164s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build2.dsc: no acceptable signature found 165s autopkgtest [12:34:51]: testing package python-biom-format version 2.1.16-1build2 168s autopkgtest [12:34:54]: build not needed 172s autopkgtest [12:34:58]: test run-unit-test: preparing testbed 174s Reading package lists... 175s Building dependency tree... 175s Reading state information... 175s Starting pkgProblemResolver with broken count: 0 175s Starting 2 pkgProblemResolver with broken count: 0 175s Done 176s The following NEW packages will be installed: 176s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 libjs-jquery 176s libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 libsz2 176s python-biom-format-doc python3-biom-format python3-click python3-dateutil 176s python3-decorator python3-h5py python3-h5py-serial python3-numpy 176s python3-pandas python3-pandas-lib python3-pytz python3-scipy python3-tz 176s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 176s Need to get 40.8 MB of archives. 176s After this operation, 191 MB of additional disk space will be used. 176s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 177s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 177s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 177s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 177s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 177s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 177s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 177s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 177s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libjs-sphinxdoc all 8.1.3-5 [31.0 kB] 177s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 177s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 177s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 177s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biom-format-doc all 2.1.16-1build2 [57.5 kB] 177s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 178s Get:15 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.12.1-1 [1489 kB] 178s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.12.1-1 [7970 B] 178s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.8-1 [79.8 kB] 178s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 178s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pytz all 2025.1-3 [162 kB] 178s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2025.1-3 [1866 B] 178s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-8 [7617 kB] 178s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-8 [3112 kB] 179s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 179s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu1 [19.5 MB] 179s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1build2 [158 kB] 180s Fetched 40.8 MB in 3s (13.5 MB/s) 180s Selecting previously unselected package libaec0:armhf. 180s (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 ... 60727 files and directories currently installed.) 180s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 180s Unpacking libaec0:armhf (1.1.3-1) ... 180s Selecting previously unselected package libblas3:armhf. 180s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 180s Unpacking libblas3:armhf (3.12.1-2) ... 180s Selecting previously unselected package libgfortran5:armhf. 180s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 180s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 180s Selecting previously unselected package libsz2:armhf. 180s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 180s Unpacking libsz2:armhf (1.1.3-1) ... 180s Selecting previously unselected package libhdf5-310:armhf. 180s Preparing to unpack .../04-libhdf5-310_1.14.5+repack-3_armhf.deb ... 180s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 180s Selecting previously unselected package libhdf5-hl-310:armhf. 180s Preparing to unpack .../05-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 180s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 180s Selecting previously unselected package libjs-jquery. 180s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 180s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 180s Selecting previously unselected package libjs-underscore. 180s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 180s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 180s Selecting previously unselected package libjs-sphinxdoc. 180s Preparing to unpack .../08-libjs-sphinxdoc_8.1.3-5_all.deb ... 180s Unpacking libjs-sphinxdoc (8.1.3-5) ... 180s Selecting previously unselected package liblapack3:armhf. 180s Preparing to unpack .../09-liblapack3_3.12.1-2_armhf.deb ... 180s Unpacking liblapack3:armhf (3.12.1-2) ... 181s Selecting previously unselected package liblbfgsb0:armhf. 181s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 181s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 181s Selecting previously unselected package liblzf1:armhf. 181s Preparing to unpack .../11-liblzf1_3.6-4_armhf.deb ... 181s Unpacking liblzf1:armhf (3.6-4) ... 181s Selecting previously unselected package python-biom-format-doc. 181s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build2_all.deb ... 181s Unpacking python-biom-format-doc (2.1.16-1build2) ... 181s Selecting previously unselected package python3-numpy. 181s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 181s Unpacking python3-numpy (1:1.26.4+ds-13) ... 181s Selecting previously unselected package python3-h5py-serial. 181s Preparing to unpack .../14-python3-h5py-serial_3.12.1-1_armhf.deb ... 181s Unpacking python3-h5py-serial (3.12.1-1) ... 181s Selecting previously unselected package python3-h5py. 181s Preparing to unpack .../15-python3-h5py_3.12.1-1_all.deb ... 181s Unpacking python3-h5py (3.12.1-1) ... 181s Selecting previously unselected package python3-click. 181s Preparing to unpack .../16-python3-click_8.1.8-1_all.deb ... 181s Unpacking python3-click (8.1.8-1) ... 181s Selecting previously unselected package python3-dateutil. 181s Preparing to unpack .../17-python3-dateutil_2.9.0-3_all.deb ... 181s Unpacking python3-dateutil (2.9.0-3) ... 181s Selecting previously unselected package python3-pytz. 181s Preparing to unpack .../18-python3-pytz_2025.1-3_all.deb ... 181s Unpacking python3-pytz (2025.1-3) ... 181s Selecting previously unselected package python3-tz. 181s Preparing to unpack .../19-python3-tz_2025.1-3_all.deb ... 181s Unpacking python3-tz (2025.1-3) ... 181s Selecting previously unselected package python3-pandas-lib:armhf. 181s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-8_armhf.deb ... 181s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 182s Selecting previously unselected package python3-pandas. 182s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-8_all.deb ... 182s Unpacking python3-pandas (2.2.3+dfsg-8) ... 182s Selecting previously unselected package python3-decorator. 182s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 182s Unpacking python3-decorator (5.1.1-5) ... 182s Selecting previously unselected package python3-scipy. 182s Preparing to unpack .../23-python3-scipy_1.14.1-4ubuntu1_armhf.deb ... 182s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 183s Selecting previously unselected package python3-biom-format. 183s Preparing to unpack .../24-python3-biom-format_2.1.16-1build2_armhf.deb ... 183s Unpacking python3-biom-format (2.1.16-1build2) ... 183s Setting up python3-pytz (2025.1-3) ... 183s Setting up python3-click (8.1.8-1) ... 183s Setting up libaec0:armhf (1.1.3-1) ... 183s Setting up python3-tz (2025.1-3) ... 183s Setting up python3-decorator (5.1.1-5) ... 184s Setting up libblas3:armhf (3.12.1-2) ... 184s 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 184s Setting up liblzf1:armhf (3.6-4) ... 184s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 184s Setting up python3-dateutil (2.9.0-3) ... 184s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 184s Setting up libsz2:armhf (1.1.3-1) ... 184s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 184s Setting up liblapack3:armhf (3.12.1-2) ... 184s 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 184s Setting up python3-numpy (1:1.26.4+ds-13) ... 188s Setting up libjs-sphinxdoc (8.1.3-5) ... 188s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 188s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 188s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 188s Setting up python3-scipy (1.14.1-4ubuntu1) ... 196s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 196s Setting up python3-h5py-serial (3.12.1-1) ... 197s Setting up python-biom-format-doc (2.1.16-1build2) ... 197s Setting up python3-pandas (2.2.3+dfsg-8) ... 208s Setting up python3-h5py (3.12.1-1) ... 208s Setting up python3-biom-format (2.1.16-1build2) ... 209s Processing triggers for man-db (2.13.0-1) ... 209s Processing triggers for libc-bin (2.40-4ubuntu1) ... 221s autopkgtest [12:35:47]: test run-unit-test: [----------------------- 224s 224s System information 224s ================== 224s Platform: linux 224s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 224s Python executable: /usr/bin/python3 224s 224s Dependency versions 224s =================== 224s click version: 8.1.8 224s NumPy version: 1.26.4 224s SciPy version: 1.14.1 224s h5py version: 3.12.1 224s 224s biom-format package information 224s =============================== 224s biom-format version: 2.1.16 224s 225s 225s The input file is a valid BIOM-formatted file. 226s 226s The input file is a valid BIOM-formatted file. 228s 228s The input file is a valid BIOM-formatted file. 229s 229s The input file is a valid BIOM-formatted file. 231s + table=examples/min_sparse_otu_table_hdf5.biom 231s + obsmd=examples/obs_md.txt 231s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 231s + biom show-install-info 232s 232s System information 232s ================== 232s Platform: linux 232s Python version: 3.13.2 (main, Feb 5 2025, 01:23:35) [GCC 14.2.0] 232s Python executable: /usr/bin/python3 232s 232s Dependency versions 232s =================== 232s click version: 8.1.8 232s NumPy version: 1.26.4 232s SciPy version: 1.14.1 232s h5py version: 3.12.1 232s 232s biom-format package information 232s =============================== 232s biom-format version: 2.1.16 232s 233s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 234s 234s The input file is a valid BIOM-formatted file. 234s + 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 235s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 236s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 237s + biom validate-table -i test_json.biom 238s 238s The input file is a valid BIOM-formatted file. 239s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 240s + biom validate-table -i test_hdf5.biom 241s 241s The input file is a valid BIOM-formatted file. 241s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 242s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 244s + biom validate-table -i test_hdf5.biom 245s 245s The input file is a valid BIOM-formatted file. 245s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 246s + biom validate-table -i test_json.biom 247s 247s The input file is a valid BIOM-formatted file. 247s + biom head -i examples/min_sparse_otu_table_hdf5.biom 248s # Constructed from biom file 248s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 248s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 248s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 248s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 248s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 248s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 248s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 249s Sample1 249s Sample2 249s Sample3 249s Sample4 249s Sample5 249s Sample6 250s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 251s + cat 251s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 252s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 253s Num samples: 6 253s Num observations: 5 253s Total count: 27 253s Table density (fraction of non-zero values): 0.500 253s 253s Counts/sample summary: 253s Min: 3.000 253s Max: 7.000 253s Median: 4.000 253s Mean: 4.500 253s Std. dev.: 1.500 253s Sample Metadata Categories: None provided 253s Observation Metadata Categories: None provided 253s 253s Counts/sample detail: 253s Sample2: 3.000 253s Sample5: 3.000 253s Sample3: 4.000 253s Sample6: 4.000 253s Sample4: 6.000 253s Sample1: 7.000 253s + cat 253s + biom from-uc -i uctest -o test_uc.biom 255s If this message was shown, then all commands executed without failure 255s + echo If this message was shown, then all commands executed without failure 255s autopkgtest [12:36:21]: test run-unit-test: -----------------------] 260s run-unit-test PASS 260s autopkgtest [12:36:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 265s autopkgtest [12:36:31]: test autodep8-python3: preparing testbed 292s autopkgtest [12:36:58]: testbed dpkg architecture: armhf 294s autopkgtest [12:37:00]: testbed apt version: 2.9.30 298s autopkgtest [12:37:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup 301s autopkgtest [12:37:07]: testbed release detected to be: plucky 310s autopkgtest [12:37:16]: updating testbed package index (apt update) 312s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [110 kB] 312s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 312s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 312s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 313s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [3120 B] 313s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [750 kB] 313s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.9 kB] 313s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.1 kB] 313s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [99.0 kB] 313s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf Packages [760 B] 313s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [636 kB] 313s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [3116 B] 313s Fetched 1693 kB in 1s (1750 kB/s) 314s Reading package lists... 321s autopkgtest [12:37:27]: upgrading testbed (apt dist-upgrade and autopurge) 323s Reading package lists... 324s Building dependency tree... 324s Reading state information... 325s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 325s Starting 2 pkgProblemResolver with broken count: 0 325s Done 326s Entering ResolveByKeep 326s 327s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 329s Reading package lists... 330s Building dependency tree... 330s Reading state information... 330s Starting pkgProblemResolver with broken count: 0 331s Starting 2 pkgProblemResolver with broken count: 0 331s Done 332s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 334s autopkgtest [12:37:40]: rebooting testbed after setup commands that affected boot 409s Reading package lists... 409s Building dependency tree... 409s Reading state information... 409s Starting pkgProblemResolver with broken count: 0 410s Starting 2 pkgProblemResolver with broken count: 0 410s Done 410s The following NEW packages will be installed: 410s libaec0 libblas3 libgfortran5 libhdf5-310 libhdf5-hl-310 liblapack3 410s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 410s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 410s python3-numpy python3-pandas python3-pandas-lib python3-pytz python3-scipy 410s python3-tz 411s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 411s Need to get 40.3 MB of archives. 411s After this operation, 190 MB of additional disk space will be used. 411s Get:1 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 411s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 411s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250213-1ubuntu1 [330 kB] 411s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 411s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-310 armhf 1.14.5+repack-3 [1410 kB] 411s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-310 armhf 1.14.5+repack-3 [58.8 kB] 411s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 411s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 411s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 411s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.1-1~exp2 [896 B] 411s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-13 [3978 kB] 411s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.12.1-1 [1489 kB] 412s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.12.1-1 [7970 B] 412s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.8-1 [79.8 kB] 412s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-3 [80.2 kB] 412s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-pytz all 2025.1-3 [162 kB] 412s Get:17 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2025.1-3 [1866 B] 412s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-8 [7617 kB] 412s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-8 [3112 kB] 412s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 412s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu1 [19.5 MB] 412s Get:22 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1build2 [158 kB] 413s Fetched 40.3 MB in 2s (19.9 MB/s) 413s Selecting previously unselected package libaec0:armhf. 413s (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 ... 60727 files and directories currently installed.) 413s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 413s Unpacking libaec0:armhf (1.1.3-1) ... 413s Selecting previously unselected package libblas3:armhf. 413s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 413s Unpacking libblas3:armhf (3.12.1-2) ... 413s Selecting previously unselected package libgfortran5:armhf. 413s Preparing to unpack .../02-libgfortran5_15-20250213-1ubuntu1_armhf.deb ... 413s Unpacking libgfortran5:armhf (15-20250213-1ubuntu1) ... 413s Selecting previously unselected package libsz2:armhf. 413s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 413s Unpacking libsz2:armhf (1.1.3-1) ... 413s Selecting previously unselected package libhdf5-310:armhf. 413s Preparing to unpack .../04-libhdf5-310_1.14.5+repack-3_armhf.deb ... 413s Unpacking libhdf5-310:armhf (1.14.5+repack-3) ... 413s Selecting previously unselected package libhdf5-hl-310:armhf. 413s Preparing to unpack .../05-libhdf5-hl-310_1.14.5+repack-3_armhf.deb ... 413s Unpacking libhdf5-hl-310:armhf (1.14.5+repack-3) ... 413s Selecting previously unselected package liblapack3:armhf. 413s Preparing to unpack .../06-liblapack3_3.12.1-2_armhf.deb ... 413s Unpacking liblapack3:armhf (3.12.1-2) ... 413s Selecting previously unselected package liblbfgsb0:armhf. 413s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 413s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 414s Selecting previously unselected package liblzf1:armhf. 414s Preparing to unpack .../08-liblzf1_3.6-4_armhf.deb ... 414s Unpacking liblzf1:armhf (3.6-4) ... 414s Selecting previously unselected package python3-all. 414s Preparing to unpack .../09-python3-all_3.13.1-1~exp2_armhf.deb ... 414s Unpacking python3-all (3.13.1-1~exp2) ... 414s Selecting previously unselected package python3-numpy. 414s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-13_armhf.deb ... 414s Unpacking python3-numpy (1:1.26.4+ds-13) ... 414s Selecting previously unselected package python3-h5py-serial. 414s Preparing to unpack .../11-python3-h5py-serial_3.12.1-1_armhf.deb ... 414s Unpacking python3-h5py-serial (3.12.1-1) ... 414s Selecting previously unselected package python3-h5py. 414s Preparing to unpack .../12-python3-h5py_3.12.1-1_all.deb ... 414s Unpacking python3-h5py (3.12.1-1) ... 414s Selecting previously unselected package python3-click. 414s Preparing to unpack .../13-python3-click_8.1.8-1_all.deb ... 414s Unpacking python3-click (8.1.8-1) ... 414s Selecting previously unselected package python3-dateutil. 414s Preparing to unpack .../14-python3-dateutil_2.9.0-3_all.deb ... 414s Unpacking python3-dateutil (2.9.0-3) ... 414s Selecting previously unselected package python3-pytz. 414s Preparing to unpack .../15-python3-pytz_2025.1-3_all.deb ... 414s Unpacking python3-pytz (2025.1-3) ... 414s Selecting previously unselected package python3-tz. 414s Preparing to unpack .../16-python3-tz_2025.1-3_all.deb ... 414s Unpacking python3-tz (2025.1-3) ... 414s Selecting previously unselected package python3-pandas-lib:armhf. 414s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-8_armhf.deb ... 414s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 414s Selecting previously unselected package python3-pandas. 415s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-8_all.deb ... 415s Unpacking python3-pandas (2.2.3+dfsg-8) ... 415s Selecting previously unselected package python3-decorator. 415s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 415s Unpacking python3-decorator (5.1.1-5) ... 415s Selecting previously unselected package python3-scipy. 415s Preparing to unpack .../20-python3-scipy_1.14.1-4ubuntu1_armhf.deb ... 415s Unpacking python3-scipy (1.14.1-4ubuntu1) ... 416s Selecting previously unselected package python3-biom-format. 416s Preparing to unpack .../21-python3-biom-format_2.1.16-1build2_armhf.deb ... 416s Unpacking python3-biom-format (2.1.16-1build2) ... 416s Setting up python3-all (3.13.1-1~exp2) ... 416s Setting up python3-pytz (2025.1-3) ... 416s Setting up python3-click (8.1.8-1) ... 416s Setting up libaec0:armhf (1.1.3-1) ... 416s Setting up python3-tz (2025.1-3) ... 416s Setting up python3-decorator (5.1.1-5) ... 416s Setting up libblas3:armhf (3.12.1-2) ... 416s 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 416s Setting up liblzf1:armhf (3.6-4) ... 416s Setting up libgfortran5:armhf (15-20250213-1ubuntu1) ... 416s Setting up python3-dateutil (2.9.0-3) ... 417s Setting up libsz2:armhf (1.1.3-1) ... 417s Setting up liblapack3:armhf (3.12.1-2) ... 417s 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 417s Setting up python3-numpy (1:1.26.4+ds-13) ... 421s Setting up libhdf5-310:armhf (1.14.5+repack-3) ... 421s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 421s Setting up libhdf5-hl-310:armhf (1.14.5+repack-3) ... 421s Setting up python3-scipy (1.14.1-4ubuntu1) ... 429s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-8) ... 429s Setting up python3-h5py-serial (3.12.1-1) ... 430s Setting up python3-pandas (2.2.3+dfsg-8) ... 442s Setting up python3-h5py (3.12.1-1) ... 442s Setting up python3-biom-format (2.1.16-1build2) ... 442s Processing triggers for man-db (2.13.0-1) ... 443s Processing triggers for libc-bin (2.40-4ubuntu1) ... 461s autopkgtest [12:39:47]: 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 461s autopkgtest [12:39:47]: test autodep8-python3: [----------------------- 464s Testing with python3.12: 465s 465s Testing with python3.13: 466s 467s autopkgtest [12:39:53]: test autodep8-python3: -----------------------] 471s autodep8-python3 PASS (superficial) 471s autopkgtest [12:39:57]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 475s autopkgtest [12:40:01]: @@@@@@@@@@@@@@@@@@@@ summary 475s run-unit-test PASS 475s autodep8-python3 PASS (superficial)