0s autopkgtest [14:37:09]: starting date and time: 2024-12-04 14:37:09+0000 0s autopkgtest [14:37:09]: git checkout: 48af33f0 Fix --add-apt-source=ppa for focal 0s autopkgtest [14:37:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ko5s5lps/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:h5py,src:openmpi --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=h5py/3.11.0-8ubuntu3 openmpi/5.0.6-3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-10.secgroup --name adt-plucky-arm64-python-biom-format-20241204-143708-juju-7f2275-prod-proposed-migration-environment-2-ec708291-ff21-4a8e-8205-ae9d106d3542 --image adt/ubuntu-plucky-arm64-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,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/ 286s autopkgtest [14:41:55]: testbed dpkg architecture: arm64 286s autopkgtest [14:41:55]: testbed apt version: 2.9.16 287s autopkgtest [14:41:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 287s autopkgtest [14:41:56]: testbed release detected to be: None 288s autopkgtest [14:41:57]: updating testbed package index (apt update) 288s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 288s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 288s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 288s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 288s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [58.3 kB] 288s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [745 kB] 289s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.2 kB] 289s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 289s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [125 kB] 289s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [58.2 kB] 289s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [617 kB] 289s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [20.8 kB] 289s Fetched 1721 kB in 1s (1804 kB/s) 290s Reading package lists... 291s Reading package lists... 291s Building dependency tree... 291s Reading state information... 292s Calculating upgrade... 292s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 292s Reading package lists... 293s Building dependency tree... 293s Reading state information... 293s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 294s autopkgtest [14:42:03]: upgrading testbed (apt dist-upgrade and autopurge) 294s Reading package lists... 294s Building dependency tree... 294s Reading state information... 295s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 295s Starting 2 pkgProblemResolver with broken count: 0 295s Done 296s Entering ResolveByKeep 296s 297s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 297s Reading package lists... 297s Building dependency tree... 297s Reading state information... 298s Starting pkgProblemResolver with broken count: 0 298s Starting 2 pkgProblemResolver with broken count: 0 298s Done 299s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 301s autopkgtest [14:42:10]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 301s autopkgtest [14:42:10]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 304s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (dsc) [2498 B] 304s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (tar) [11.9 MB] 304s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1build1 (diff) [11.6 kB] 305s gpgv: Signature made Fri Nov 15 13:41:43 2024 UTC 305s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 305s gpgv: Can't check signature: No public key 305s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1build1.dsc: no acceptable signature found 305s autopkgtest [14:42:14]: testing package python-biom-format version 2.1.16-1build1 306s autopkgtest [14:42:15]: build not needed 308s autopkgtest [14:42:17]: test run-unit-test: preparing testbed 309s Reading package lists... 309s Building dependency tree... 309s Reading state information... 309s Starting pkgProblemResolver with broken count: 0 309s Starting 2 pkgProblemResolver with broken count: 0 309s Done 310s The following NEW packages will be installed: 310s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 310s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 310s libsz2 python-biom-format-doc python3-biom-format python3-click 310s python3-colorama python3-dateutil python3-decorator python3-h5py 310s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 310s python3-scipy python3-tz 311s 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. 311s Need to get 40.0 MB of archives. 311s After this operation, 222 MB of additional disk space will be used. 311s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 311s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 311s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-9ubuntu1 [437 kB] 311s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 311s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 311s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 311s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 311s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 311s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB] 311s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 312s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 312s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 312s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1build1 [57.9 kB] 312s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 313s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 313s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 313s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 313s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 313s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 313s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 313s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB] 315s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 315s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 315s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5ubuntu1 [19.1 MB] 319s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build1 [165 kB] 319s Fetched 40.0 MB in 8s (4836 kB/s) 319s Selecting previously unselected package libaec0:arm64. 320s (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 ... 80338 files and directories currently installed.) 320s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 320s Unpacking libaec0:arm64 (1.1.3-1) ... 320s Selecting previously unselected package libblas3:arm64. 320s Preparing to unpack .../01-libblas3_3.12.0-4_arm64.deb ... 320s Unpacking libblas3:arm64 (3.12.0-4) ... 320s Selecting previously unselected package libgfortran5:arm64. 320s Preparing to unpack .../02-libgfortran5_14.2.0-9ubuntu1_arm64.deb ... 320s Unpacking libgfortran5:arm64 (14.2.0-9ubuntu1) ... 320s Selecting previously unselected package libsz2:arm64. 320s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 320s Unpacking libsz2:arm64 (1.1.3-1) ... 320s Selecting previously unselected package libhdf5-103-1t64:arm64. 320s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 320s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 320s Selecting previously unselected package libhdf5-hl-100t64:arm64. 320s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 320s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 320s Selecting previously unselected package libjs-jquery. 320s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 320s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 320s Selecting previously unselected package libjs-underscore. 320s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 320s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 320s Selecting previously unselected package libjs-sphinxdoc. 320s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 320s Unpacking libjs-sphinxdoc (7.4.7-4) ... 320s Selecting previously unselected package liblapack3:arm64. 320s Preparing to unpack .../09-liblapack3_3.12.0-4_arm64.deb ... 320s Unpacking liblapack3:arm64 (3.12.0-4) ... 320s Selecting previously unselected package liblbfgsb0:arm64. 320s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 320s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 321s Selecting previously unselected package liblzf1:arm64. 321s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ... 321s Unpacking liblzf1:arm64 (3.6-4) ... 321s Selecting previously unselected package python-biom-format-doc. 321s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1build1_all.deb ... 321s Unpacking python-biom-format-doc (2.1.16-1build1) ... 321s Selecting previously unselected package python3-numpy. 321s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 321s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 321s Selecting previously unselected package python3-h5py-serial. 321s Preparing to unpack .../14-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 321s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 321s Selecting previously unselected package python3-h5py. 321s Preparing to unpack .../15-python3-h5py_3.11.0-8ubuntu3_all.deb ... 321s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 321s Selecting previously unselected package python3-colorama. 321s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 321s Unpacking python3-colorama (0.4.6-4) ... 321s Selecting previously unselected package python3-click. 321s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 321s Unpacking python3-click (8.1.7-2) ... 321s Selecting previously unselected package python3-dateutil. 321s Preparing to unpack .../18-python3-dateutil_2.9.0-3_all.deb ... 321s Unpacking python3-dateutil (2.9.0-3) ... 321s Selecting previously unselected package python3-tz. 321s Preparing to unpack .../19-python3-tz_2024.1-2_all.deb ... 321s Unpacking python3-tz (2024.1-2) ... 321s Selecting previously unselected package python3-pandas-lib:arm64. 322s Preparing to unpack .../20-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ... 322s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 322s Selecting previously unselected package python3-pandas. 322s Preparing to unpack .../21-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 322s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 322s Selecting previously unselected package python3-decorator. 322s Preparing to unpack .../22-python3-decorator_5.1.1-5_all.deb ... 322s Unpacking python3-decorator (5.1.1-5) ... 322s Selecting previously unselected package python3-scipy. 322s Preparing to unpack .../23-python3-scipy_1.13.1-5ubuntu1_arm64.deb ... 322s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 323s Selecting previously unselected package python3-biom-format. 323s Preparing to unpack .../24-python3-biom-format_2.1.16-1build1_arm64.deb ... 323s Unpacking python3-biom-format (2.1.16-1build1) ... 323s Setting up python3-colorama (0.4.6-4) ... 323s Setting up python3-click (8.1.7-2) ... 323s Setting up libaec0:arm64 (1.1.3-1) ... 323s Setting up python3-tz (2024.1-2) ... 324s Setting up python3-decorator (5.1.1-5) ... 324s Setting up libblas3:arm64 (3.12.0-4) ... 324s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 324s Setting up liblzf1:arm64 (3.6-4) ... 324s Setting up libgfortran5:arm64 (14.2.0-9ubuntu1) ... 324s Setting up python3-dateutil (2.9.0-3) ... 324s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 324s Setting up libsz2:arm64 (1.1.3-1) ... 324s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 324s Setting up liblapack3:arm64 (3.12.0-4) ... 324s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 324s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 327s Setting up libjs-sphinxdoc (7.4.7-4) ... 327s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 327s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 327s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 327s Setting up python3-scipy (1.13.1-5ubuntu1) ... 331s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 331s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 331s Setting up python-biom-format-doc (2.1.16-1build1) ... 331s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 337s Setting up python3-h5py (3.11.0-8ubuntu3) ... 337s Setting up python3-biom-format (2.1.16-1build1) ... 337s Processing triggers for man-db (2.13.0-1) ... 338s Processing triggers for libc-bin (2.40-1ubuntu3) ... 339s autopkgtest [14:42:48]: test run-unit-test: [----------------------- 341s 341s System information 341s ================== 341s Platform: linux 341s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 341s Python executable: /usr/bin/python3 341s 341s Dependency versions 341s =================== 341s click version: 8.1.7 341s NumPy version: 1.26.4 341s SciPy version: 1.13.1 341s h5py version: 3.11.0 341s 341s biom-format package information 341s =============================== 341s biom-format version: 2.1.16 341s 342s 342s The input file is a valid BIOM-formatted file. 343s 343s The input file is a valid BIOM-formatted file. 344s 344s The input file is a valid BIOM-formatted file. 345s 345s The input file is a valid BIOM-formatted file. 348s + table=examples/min_sparse_otu_table_hdf5.biom 348s + obsmd=examples/obs_md.txt 348s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 348s + biom show-install-info 349s 349s System information 349s ================== 349s Platform: linux 349s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 349s Python executable: /usr/bin/python3 349s 349s Dependency versions 349s =================== 349s click version: 8.1.7 349s NumPy version: 1.26.4 349s SciPy version: 1.13.1 349s h5py version: 3.11.0 349s 349s biom-format package information 349s =============================== 349s biom-format version: 2.1.16 349s 349s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 350s 350s The input file is a valid BIOM-formatted file. 350s + 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 351s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 352s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 354s + biom validate-table -i test_json.biom 354s 354s The input file is a valid BIOM-formatted file. 355s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 356s + biom validate-table -i test_hdf5.biom 357s 357s The input file is a valid BIOM-formatted file. 357s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 358s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 359s + biom validate-table -i test_hdf5.biom 360s 360s The input file is a valid BIOM-formatted file. 360s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 361s + biom validate-table -i test_json.biom 362s 362s The input file is a valid BIOM-formatted file. 362s + biom head -i examples/min_sparse_otu_table_hdf5.biom 363s # Constructed from biom file 363s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 363s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 363s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 363s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 363s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 363s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 364s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 365s Sample1 365s Sample2 365s Sample3 365s Sample4 365s Sample5 365s Sample6 365s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 366s + cat 366s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 367s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 368s Num samples: 6 368s Num observations: 5 368s Total count: 27 368s Table density (fraction of non-zero values): 0.500 368s 368s Counts/sample summary: 368s Min: 3.000 368s Max: 7.000 368s Median: 4.000 368s Mean: 4.500 368s Std. dev.: 1.500 368s Sample Metadata Categories: None provided 368s Observation Metadata Categories: None provided 368s 368s Counts/sample detail: 368s Sample2: 3.000 368s Sample5: 3.000 368s Sample3: 4.000 368s Sample6: 4.000 368s Sample4: 6.000 368s Sample1: 7.000 368s + cat 368s + biom from-uc -i uctest -o test_uc.biom 369s If this message was shown, then all commands executed without failure 369s + echo If this message was shown, then all commands executed without failure 369s autopkgtest [14:43:18]: test run-unit-test: -----------------------] 370s autopkgtest [14:43:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 370s run-unit-test PASS 370s autopkgtest [14:43:19]: test autodep8-python3: preparing testbed 509s autopkgtest [14:45:38]: testbed dpkg architecture: arm64 509s autopkgtest [14:45:38]: testbed apt version: 2.9.16 509s autopkgtest [14:45:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 509s autopkgtest [14:45:38]: testbed release detected to be: plucky 510s autopkgtest [14:45:39]: updating testbed package index (apt update) 510s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 511s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 511s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 511s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 511s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [14.2 kB] 511s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [58.3 kB] 511s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 511s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [745 kB] 511s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [125 kB] 511s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [58.2 kB] 511s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [617 kB] 511s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [20.8 kB] 511s Fetched 1721 kB in 1s (1587 kB/s) 512s Reading package lists... 513s Reading package lists... 513s Building dependency tree... 513s Reading state information... 514s Calculating upgrade... 514s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 514s Reading package lists... 515s Building dependency tree... 515s Reading state information... 515s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 515s autopkgtest [14:45:44]: upgrading testbed (apt dist-upgrade and autopurge) 515s Reading package lists... 516s Building dependency tree... 516s Reading state information... 516s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 516s Starting 2 pkgProblemResolver with broken count: 0 516s Done 517s Entering ResolveByKeep 517s 518s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 518s Reading package lists... 518s Building dependency tree... 518s Reading state information... 519s Starting pkgProblemResolver with broken count: 0 519s Starting 2 pkgProblemResolver with broken count: 0 519s Done 520s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 523s Reading package lists... 523s Building dependency tree... 523s Reading state information... 523s Starting pkgProblemResolver with broken count: 0 523s Starting 2 pkgProblemResolver with broken count: 0 523s Done 524s The following NEW packages will be installed: 524s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 524s liblbfgsb0 liblzf1 libsz2 python3-all python3-biom-format python3-click 524s python3-colorama python3-dateutil python3-decorator python3-h5py 524s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 524s python3-scipy python3-tz 524s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 524s Need to get 39.3 MB of archives. 524s After this operation, 220 MB of additional disk space will be used. 524s Get:1 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 525s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-4 [152 kB] 525s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-9ubuntu1 [437 kB] 525s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 525s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB] 525s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB] 525s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-4 [2305 kB] 525s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 525s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 525s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 525s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11ubuntu1 [4149 kB] 525s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py-serial arm64 3.11.0-8ubuntu3 [1452 kB] 525s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 python3-h5py all 3.11.0-8ubuntu3 [7982 B] 525s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB] 525s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB] 525s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-3 [80.2 kB] 525s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB] 525s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5ubuntu1 [6921 kB] 525s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5ubuntu1 [3112 kB] 525s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 525s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5ubuntu1 [19.1 MB] 526s Get:22 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1build1 [165 kB] 526s Fetched 39.3 MB in 2s (22.5 MB/s) 526s Selecting previously unselected package libaec0:arm64. 527s (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 ... 80338 files and directories currently installed.) 527s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ... 527s Unpacking libaec0:arm64 (1.1.3-1) ... 527s Selecting previously unselected package libblas3:arm64. 527s Preparing to unpack .../01-libblas3_3.12.0-4_arm64.deb ... 527s Unpacking libblas3:arm64 (3.12.0-4) ... 527s Selecting previously unselected package libgfortran5:arm64. 527s Preparing to unpack .../02-libgfortran5_14.2.0-9ubuntu1_arm64.deb ... 527s Unpacking libgfortran5:arm64 (14.2.0-9ubuntu1) ... 527s Selecting previously unselected package libsz2:arm64. 527s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ... 527s Unpacking libsz2:arm64 (1.1.3-1) ... 527s Selecting previously unselected package libhdf5-103-1t64:arm64. 527s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ... 527s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 527s Selecting previously unselected package libhdf5-hl-100t64:arm64. 527s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ... 527s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 527s Selecting previously unselected package liblapack3:arm64. 527s Preparing to unpack .../06-liblapack3_3.12.0-4_arm64.deb ... 527s Unpacking liblapack3:arm64 (3.12.0-4) ... 527s Selecting previously unselected package liblbfgsb0:arm64. 527s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 527s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 527s Selecting previously unselected package liblzf1:arm64. 527s Preparing to unpack .../08-liblzf1_3.6-4_arm64.deb ... 527s Unpacking liblzf1:arm64 (3.6-4) ... 527s Selecting previously unselected package python3-all. 527s Preparing to unpack .../09-python3-all_3.12.6-0ubuntu1_arm64.deb ... 527s Unpacking python3-all (3.12.6-0ubuntu1) ... 527s Selecting previously unselected package python3-numpy. 527s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11ubuntu1_arm64.deb ... 527s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ... 527s Selecting previously unselected package python3-h5py-serial. 527s Preparing to unpack .../11-python3-h5py-serial_3.11.0-8ubuntu3_arm64.deb ... 527s Unpacking python3-h5py-serial (3.11.0-8ubuntu3) ... 528s Selecting previously unselected package python3-h5py. 528s Preparing to unpack .../12-python3-h5py_3.11.0-8ubuntu3_all.deb ... 528s Unpacking python3-h5py (3.11.0-8ubuntu3) ... 528s Selecting previously unselected package python3-colorama. 528s Preparing to unpack .../13-python3-colorama_0.4.6-4_all.deb ... 528s Unpacking python3-colorama (0.4.6-4) ... 528s Selecting previously unselected package python3-click. 528s Preparing to unpack .../14-python3-click_8.1.7-2_all.deb ... 528s Unpacking python3-click (8.1.7-2) ... 528s Selecting previously unselected package python3-dateutil. 528s Preparing to unpack .../15-python3-dateutil_2.9.0-3_all.deb ... 528s Unpacking python3-dateutil (2.9.0-3) ... 528s Selecting previously unselected package python3-tz. 528s Preparing to unpack .../16-python3-tz_2024.1-2_all.deb ... 528s Unpacking python3-tz (2024.1-2) ... 528s Selecting previously unselected package python3-pandas-lib:arm64. 528s Preparing to unpack .../17-python3-pandas-lib_2.2.3+dfsg-5ubuntu1_arm64.deb ... 528s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 528s Selecting previously unselected package python3-pandas. 528s Preparing to unpack .../18-python3-pandas_2.2.3+dfsg-5ubuntu1_all.deb ... 528s Unpacking python3-pandas (2.2.3+dfsg-5ubuntu1) ... 528s Selecting previously unselected package python3-decorator. 528s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 528s Unpacking python3-decorator (5.1.1-5) ... 528s Selecting previously unselected package python3-scipy. 528s Preparing to unpack .../20-python3-scipy_1.13.1-5ubuntu1_arm64.deb ... 528s Unpacking python3-scipy (1.13.1-5ubuntu1) ... 529s Selecting previously unselected package python3-biom-format. 529s Preparing to unpack .../21-python3-biom-format_2.1.16-1build1_arm64.deb ... 529s Unpacking python3-biom-format (2.1.16-1build1) ... 529s Setting up python3-colorama (0.4.6-4) ... 529s Setting up python3-all (3.12.6-0ubuntu1) ... 529s Setting up python3-click (8.1.7-2) ... 529s Setting up libaec0:arm64 (1.1.3-1) ... 529s Setting up python3-tz (2024.1-2) ... 529s Setting up python3-decorator (5.1.1-5) ... 529s Setting up libblas3:arm64 (3.12.0-4) ... 529s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 529s Setting up liblzf1:arm64 (3.6-4) ... 529s Setting up libgfortran5:arm64 (14.2.0-9ubuntu1) ... 529s Setting up python3-dateutil (2.9.0-3) ... 530s Setting up libsz2:arm64 (1.1.3-1) ... 530s Setting up liblapack3:arm64 (3.12.0-4) ... 530s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 530s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ... 532s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ... 532s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 532s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ... 532s Setting up python3-scipy (1.13.1-5ubuntu1) ... 535s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5ubuntu1) ... 535s Setting up python3-h5py-serial (3.11.0-8ubuntu3) ... 536s Setting up python3-pandas (2.2.3+dfsg-5ubuntu1) ... 541s Setting up python3-h5py (3.11.0-8ubuntu3) ... 542s Setting up python3-biom-format (2.1.16-1build1) ... 542s Processing triggers for man-db (2.13.0-1) ... 543s Processing triggers for libc-bin (2.40-1ubuntu3) ... 547s autopkgtest [14:46:16]: 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 547s autopkgtest [14:46:16]: test autodep8-python3: [----------------------- 547s Testing with python3.12: 549s 549s autopkgtest [14:46:18]: test autodep8-python3: -----------------------] 550s autodep8-python3 PASS (superficial) 550s autopkgtest [14:46:19]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 550s autopkgtest [14:46:19]: @@@@@@@@@@@@@@@@@@@@ summary 550s run-unit-test PASS 550s autodep8-python3 PASS (superficial) 639s nova [W] Using flock in prodstack6-arm64 639s flock: timeout while waiting to get lock 639s Creating nova instance adt-plucky-arm64-python-biom-format-20241204-143708-juju-7f2275-prod-proposed-migration-environment-2-ec708291-ff21-4a8e-8205-ae9d106d3542 from image adt/ubuntu-plucky-arm64-server-20241204.img (UUID b1e2b1c6-409a-4f80-af2b-468b6b2bbda4)... 639s nova [W] Using flock in prodstack6-arm64 639s Creating nova instance adt-plucky-arm64-python-biom-format-20241204-143708-juju-7f2275-prod-proposed-migration-environment-2-ec708291-ff21-4a8e-8205-ae9d106d3542 from image adt/ubuntu-plucky-arm64-server-20241204.img (UUID b1e2b1c6-409a-4f80-af2b-468b6b2bbda4)...