0s autopkgtest [10:39:13]: starting date and time: 2024-11-13 10:39:13+0000
  0s autopkgtest [10:39:13]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [10:39:13]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u6h2_1mo/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade python-biom-format --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-16.secgroup --name adt-plucky-amd64-python-biom-format-20241113-103913-juju-7f2275-prod-proposed-migration-environment-15-bcfe9594-ab41-4f37-b684-45e4d8aed9b5 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/
1497s autopkgtest [11:04:10]: testbed dpkg architecture: amd64
1498s autopkgtest [11:04:11]: testbed apt version: 2.9.8
1498s autopkgtest [11:04:11]: @@@@@@@@@@@@@@@@@@@@ test bed setup
1499s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
1499s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
1500s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
1500s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
1500s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
1500s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB]
1500s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB]
1500s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
1500s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB]
1500s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB]
1500s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB]
1500s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB]
1500s Fetched 2175 kB in 1s (1994 kB/s)
1500s Reading package lists...
1503s Reading package lists...
1503s Building dependency tree...
1503s Reading state information...
1503s Calculating upgrade...
1504s The following NEW packages will be installed:
1504s   python3.13-gdbm
1504s The following packages will be upgraded:
1504s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
1504s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
1504s Need to get 253 kB of archives.
1504s After this operation, 147 kB of additional disk space will be used.
1504s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
1504s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
1504s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
1504s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
1504s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
1504s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB]
1504s Fetched 253 kB in 0s (610 kB/s)
1505s (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 ... 75541 files and directories currently installed.)
1505s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
1505s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
1505s Setting up python3-minimal (3.12.7-1) ...
1505s (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 ... 75541 files and directories currently installed.)
1505s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
1505s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
1505s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
1505s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
1505s Selecting previously unselected package python3.13-gdbm.
1505s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
1505s Unpacking python3.13-gdbm (3.13.0-2) ...
1505s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
1505s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
1505s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ...
1505s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
1505s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ...
1505s Setting up python3.13-gdbm (3.13.0-2) ...
1505s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
1505s Setting up python3 (3.12.7-1) ...
1505s Setting up python3-gdbm:amd64 (3.12.7-1) ...
1505s Processing triggers for man-db (2.12.1-3) ...
1506s Processing triggers for libc-bin (2.40-1ubuntu3) ...
1506s Reading package lists...
1506s Building dependency tree...
1506s Reading state information...
1506s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1507s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
1507s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
1507s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
1507s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
1508s Reading package lists...
1508s Reading package lists...
1509s Building dependency tree...
1509s Reading state information...
1509s Calculating upgrade...
1509s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1509s Reading package lists...
1509s Building dependency tree...
1509s Reading state information...
1509s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1513s autopkgtest [11:04:26]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024
1513s autopkgtest [11:04:26]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format
1516s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B]
1516s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB]
1516s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB]
1517s gpgv: Signature made Mon May 27 20:43:46 2024 UTC
1517s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
1517s gpgv:                issuer "emollier@debian.org"
1517s gpgv: Can't check signature: No public key
1517s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found
1517s autopkgtest [11:04:30]: testing package python-biom-format version 2.1.16-1
1518s autopkgtest [11:04:31]: build not needed
1521s autopkgtest [11:04:34]: test run-unit-test: preparing testbed
1524s Reading package lists...
1524s Building dependency tree...
1524s Reading state information...
1525s Starting pkgProblemResolver with broken count: 0
1525s Starting 2 pkgProblemResolver with broken count: 0
1525s Done
1525s The following additional packages will be installed:
1525s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64
1525s   libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
1525s   libsz2 python-biom-format-doc python3-biom-format python3-click
1525s   python3-colorama python3-dateutil python3-decorator python3-h5py
1525s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
1525s   python3-scipy python3-six python3-tz
1525s Suggested packages:
1525s   python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
1525s   python-pandas-doc python3-statsmodels python-scipy-doc
1525s Recommended packages:
1525s   javascript-common python3-matplotlib python3-bottleneck python3-numexpr
1525s   python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml
1525s   python3-tables python3-numba g++ | c++-compiler python3-pil
1525s The following NEW packages will be installed:
1525s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
1525s   libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
1525s   liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format
1525s   python3-click python3-colorama python3-dateutil python3-decorator
1525s   python3-h5py python3-h5py-serial python3-numpy python3-pandas
1525s   python3-pandas-lib python3-scipy python3-six python3-tz
1525s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
1525s Need to get 38.2 MB/38.2 MB of archives.
1525s After this operation, 170 MB of additional disk space will be used.
1525s Get:1 /tmp/autopkgtest.BDzhee/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [720 B]
1525s Get:2 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
1525s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
1525s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
1526s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
1526s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB]
1526s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB]
1526s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
1526s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
1526s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
1526s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
1526s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
1526s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B]
1526s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python-biom-format-doc all 2.1.16-1 [57.5 kB]
1526s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
1526s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB]
1526s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
1526s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB]
1526s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB]
1526s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB]
1526s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB]
1526s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB]
1526s Get:23 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB]
1526s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
1526s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
1526s Get:26 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
1527s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB]
1527s Fetched 38.2 MB in 2s (16.8 MB/s)
1527s Selecting previously unselected package libaec0:amd64.
1527s (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 ... 75548 files and directories currently installed.)
1527s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ...
1527s Unpacking libaec0:amd64 (1.1.3-1) ...
1527s Selecting previously unselected package libblas3:amd64.
1527s Preparing to unpack .../01-libblas3_3.12.0-3build2_amd64.deb ...
1527s Unpacking libblas3:amd64 (3.12.0-3build2) ...
1527s Selecting previously unselected package libgfortran5:amd64.
1527s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
1527s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
1528s Selecting previously unselected package libsz2:amd64.
1528s Preparing to unpack .../03-libsz2_1.1.3-1_amd64.deb ...
1528s Unpacking libsz2:amd64 (1.1.3-1) ...
1528s Selecting previously unselected package libhdf5-103-1t64:amd64.
1528s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ...
1528s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
1528s Selecting previously unselected package libhdf5-hl-100t64:amd64.
1528s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ...
1528s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ...
1528s Selecting previously unselected package libjs-jquery.
1528s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
1528s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1528s Selecting previously unselected package libjs-underscore.
1528s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
1528s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1528s Selecting previously unselected package libjs-sphinxdoc.
1528s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ...
1528s Unpacking libjs-sphinxdoc (7.4.7-4) ...
1528s Selecting previously unselected package liblapack3:amd64.
1528s Preparing to unpack .../09-liblapack3_3.12.0-3build2_amd64.deb ...
1528s Unpacking liblapack3:amd64 (3.12.0-3build2) ...
1528s Selecting previously unselected package liblbfgsb0:amd64.
1528s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ...
1528s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
1528s Selecting previously unselected package liblzf1:amd64.
1528s Preparing to unpack .../11-liblzf1_3.6-4_amd64.deb ...
1528s Unpacking liblzf1:amd64 (3.6-4) ...
1528s Selecting previously unselected package python-biom-format-doc.
1528s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ...
1528s Unpacking python-biom-format-doc (2.1.16-1) ...
1528s Selecting previously unselected package python3-numpy.
1528s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ...
1528s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
1528s Selecting previously unselected package python3-h5py-serial.
1528s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ...
1528s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
1528s Selecting previously unselected package python3-h5py.
1528s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ...
1528s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
1528s Selecting previously unselected package python3-colorama.
1528s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ...
1528s Unpacking python3-colorama (0.4.6-4) ...
1528s Selecting previously unselected package python3-click.
1528s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ...
1528s Unpacking python3-click (8.1.7-2) ...
1528s Selecting previously unselected package python3-six.
1528s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ...
1528s Unpacking python3-six (1.16.0-7) ...
1528s Selecting previously unselected package python3-dateutil.
1528s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ...
1528s Unpacking python3-dateutil (2.9.0-2) ...
1528s Selecting previously unselected package python3-tz.
1528s Preparing to unpack .../20-python3-tz_2024.1-2_all.deb ...
1528s Unpacking python3-tz (2024.1-2) ...
1528s Selecting previously unselected package python3-pandas-lib:amd64.
1528s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ...
1528s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ...
1528s Selecting previously unselected package python3-pandas.
1528s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-5_all.deb ...
1528s Unpacking python3-pandas (2.2.3+dfsg-5) ...
1529s Selecting previously unselected package python3-decorator.
1529s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ...
1529s Unpacking python3-decorator (5.1.1-5) ...
1529s Selecting previously unselected package python3-scipy.
1529s Preparing to unpack .../24-python3-scipy_1.13.1-5_amd64.deb ...
1529s Unpacking python3-scipy (1.13.1-5) ...
1529s Selecting previously unselected package python3-biom-format.
1529s Preparing to unpack .../25-python3-biom-format_2.1.16-1_amd64.deb ...
1529s Unpacking python3-biom-format (2.1.16-1) ...
1529s Selecting previously unselected package autopkgtest-satdep.
1529s Preparing to unpack .../26-1-autopkgtest-satdep.deb ...
1529s Unpacking autopkgtest-satdep (0) ...
1529s Setting up python3-colorama (0.4.6-4) ...
1529s Setting up python3-click (8.1.7-2) ...
1529s Setting up libaec0:amd64 (1.1.3-1) ...
1529s Setting up python3-tz (2024.1-2) ...
1529s Setting up python3-six (1.16.0-7) ...
1529s Setting up python3-decorator (5.1.1-5) ...
1530s Setting up libblas3:amd64 (3.12.0-3build2) ...
1530s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
1530s Setting up liblzf1:amd64 (3.6-4) ...
1530s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
1530s Setting up python3-dateutil (2.9.0-2) ...
1530s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1530s Setting up libsz2:amd64 (1.1.3-1) ...
1530s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1530s Setting up liblapack3:amd64 (3.12.0-3build2) ...
1530s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
1530s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
1531s Setting up libjs-sphinxdoc (7.4.7-4) ...
1531s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
1531s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
1531s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ...
1531s Setting up python3-scipy (1.13.1-5) ...
1533s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ...
1533s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
1534s Setting up python-biom-format-doc (2.1.16-1) ...
1534s Setting up python3-pandas (2.2.3+dfsg-5) ...
1537s Setting up python3-h5py (3.11.0-5ubuntu1) ...
1538s Setting up python3-biom-format (2.1.16-1) ...
1538s Setting up autopkgtest-satdep (0) ...
1538s Processing triggers for man-db (2.12.1-3) ...
1538s Processing triggers for libc-bin (2.40-1ubuntu3) ...
1541s (Reading database ... 80061 files and directories currently installed.)
1541s Removing autopkgtest-satdep (0) ...
1541s autopkgtest [11:04:54]: test run-unit-test: [-----------------------
1542s 
1542s System information
1542s ==================
1542s          Platform:	linux
1542s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
1542s Python executable:	/usr/bin/python3
1542s 
1542s Dependency versions
1542s ===================
1542s click version:	8.1.7
1542s NumPy version:	1.26.4
1542s SciPy version:	1.13.1
1542s  h5py version:	3.11.0
1542s 
1542s biom-format package information
1542s ===============================
1542s biom-format version:	2.1.16
1542s 
1543s 
1543s The input file is a valid BIOM-formatted file.
1543s 
1543s The input file is a valid BIOM-formatted file.
1544s 
1544s The input file is a valid BIOM-formatted file.
1545s 
1545s The input file is a valid BIOM-formatted file.
1546s + table=examples/min_sparse_otu_table_hdf5.biom
1546s + obsmd=examples/obs_md.txt
1546s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
1546s + biom show-install-info
1546s 
1546s System information
1546s ==================
1546s          Platform:	linux
1546s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
1546s Python executable:	/usr/bin/python3
1546s 
1546s Dependency versions
1546s ===================
1546s click version:	8.1.7
1546s NumPy version:	1.26.4
1546s SciPy version:	1.13.1
1546s  h5py version:	3.11.0
1546s 
1546s biom-format package information
1546s ===============================
1546s biom-format version:	2.1.16
1546s 
1547s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
1547s 
1547s The input file is a valid BIOM-formatted file.
1547s + 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
1548s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json
1548s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv
1549s + biom validate-table -i test_json.biom
1549s 
1549s The input file is a valid BIOM-formatted file.
1550s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
1550s + biom validate-table -i test_hdf5.biom
1551s 
1551s The input file is a valid BIOM-formatted file.
1551s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv
1551s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table
1552s + biom validate-table -i test_hdf5.biom
1552s 
1552s The input file is a valid BIOM-formatted file.
1553s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table
1553s + biom validate-table -i test_json.biom
1554s 
1554s The input file is a valid BIOM-formatted file.
1554s + biom head -i examples/min_sparse_otu_table_hdf5.biom
1554s # Constructed from biom file
1554s #OTU ID	Sample1	Sample2	Sample3	Sample4	Sample5
1554s GG_OTU_1	0.0	0.0	1.0	0.0	0.0
1554s GG_OTU_2	5.0	1.0	0.0	2.0	3.0
1554s GG_OTU_3	0.0	0.0	1.0	4.0	0.0
1554s GG_OTU_4	2.0	1.0	1.0	0.0	0.0
1554s GG_OTU_5	0.0	1.0	1.0	0.0	0.0
1554s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
1555s Sample1
1555s Sample2
1555s Sample3
1555s Sample4
1555s Sample5
1555s Sample6
1555s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p
1556s + cat
1556s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt
1556s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
1557s Num samples: 6
1557s Num observations: 5
1557s Total count: 27
1557s Table density (fraction of non-zero values): 0.500
1557s 
1557s Counts/sample summary:
1557s  Min: 3.000
1557s  Max: 7.000
1557s  Median: 4.000
1557s  Mean: 4.500
1557s  Std. dev.: 1.500
1557s  Sample Metadata Categories: None provided
1557s  Observation Metadata Categories: None provided
1557s 
1557s Counts/sample detail:
1557s Sample2: 3.000
1557s Sample5: 3.000
1557s Sample3: 4.000
1557s Sample6: 4.000
1557s Sample4: 6.000
1557s Sample1: 7.000
1557s + cat
1557s + biom from-uc -i uctest -o test_uc.biom
1557s If this message was shown, then all commands executed without failure
1557s + echo If this message was shown, then all commands executed without failure
1558s autopkgtest [11:05:11]: test run-unit-test: -----------------------]
1558s autopkgtest [11:05:11]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
1558s run-unit-test        PASS
1559s autopkgtest [11:05:12]: test autodep8-python3: preparing testbed
3218s autopkgtest [11:32:51]: testbed dpkg architecture: amd64
3218s autopkgtest [11:32:51]: testbed apt version: 2.9.8
3218s autopkgtest [11:32:51]: @@@@@@@@@@@@@@@@@@@@ test bed setup
3220s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
3221s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
3221s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
3221s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
3221s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
3221s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB]
3221s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB]
3221s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB]
3221s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [639 kB]
3221s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB]
3221s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB]
3221s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB]
3221s Fetched 2175 kB in 2s (1257 kB/s)
3221s Reading package lists...
3224s Reading package lists...
3224s Building dependency tree...
3224s Reading state information...
3225s Calculating upgrade...
3225s The following NEW packages will be installed:
3225s   python3.13-gdbm
3225s The following packages will be upgraded:
3225s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
3226s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
3226s Need to get 253 kB of archives.
3226s After this operation, 147 kB of additional disk space will be used.
3226s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB]
3226s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB]
3226s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB]
3226s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB]
3226s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B]
3226s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB]
3227s Fetched 253 kB in 2s (144 kB/s)
3227s (Reading database ... 
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(Reading database ... 75541 files and directories currently installed.)
3227s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ...
3227s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
3227s Setting up python3-minimal (3.12.7-1) ...
3227s (Reading database ... 
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3227s Preparing to unpack .../python3_3.12.7-1_amd64.deb ...
3227s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
3227s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ...
3227s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
3227s Selecting previously unselected package python3.13-gdbm.
3227s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ...
3227s Unpacking python3.13-gdbm (3.13.0-2) ...
3227s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ...
3227s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
3227s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ...
3227s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
3227s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ...
3227s Setting up python3.13-gdbm (3.13.0-2) ...
3227s Setting up libpython3-stdlib:amd64 (3.12.7-1) ...
3227s Setting up python3 (3.12.7-1) ...
3228s Setting up python3-gdbm:amd64 (3.12.7-1) ...
3228s Processing triggers for man-db (2.12.1-3) ...
3228s Processing triggers for libc-bin (2.40-1ubuntu3) ...
3228s Reading package lists...
3228s Building dependency tree...
3228s Reading state information...
3229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3229s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
3229s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
3229s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
3229s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
3230s Reading package lists...
3230s Reading package lists...
3230s Building dependency tree...
3230s Reading state information...
3231s Calculating upgrade...
3231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3231s Reading package lists...
3231s Building dependency tree...
3231s Reading state information...
3231s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
3239s Reading package lists...
3239s Building dependency tree...
3239s Reading state information...
3239s Starting pkgProblemResolver with broken count: 0
3239s Starting 2 pkgProblemResolver with broken count: 0
3239s Done
3239s The following additional packages will be installed:
3239s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3
3239s   liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2
3239s   python3-all python3-biom-format python3-click python3-colorama
3239s   python3-dateutil python3-decorator python3-h5py python3-h5py-serial
3239s   python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-six
3239s   python3-tz python3.13 python3.13-minimal
3239s Suggested packages:
3239s   python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc
3239s   python3-dev python3-pytest python-pandas-doc python3-statsmodels
3239s   python-scipy-doc python3.13-venv python3.13-doc binfmt-support
3239s Recommended packages:
3239s   python3-matplotlib python3-bottleneck python3-numexpr python3-odf
3239s   python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables
3239s   python3-numba g++ | c++-compiler python3-pil
3239s The following NEW packages will be installed:
3239s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
3239s   libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal
3239s   libpython3.13-stdlib libsz2 python3-all python3-biom-format python3-click
3239s   python3-colorama python3-dateutil python3-decorator python3-h5py
3239s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
3239s   python3-scipy python3-six python3-tz python3.13 python3.13-minimal
3239s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
3239s Need to get 43.5 MB/43.5 MB of archives.
3239s After this operation, 190 MB of additional disk space will be used.
3239s Get:1 /tmp/autopkgtest.BDzhee/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B]
3240s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB]
3240s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB]
3240s Get:4 http://ftpmaster.internal/ubuntu plucky/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB]
3240s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB]
3240s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB]
3240s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 libsz2 amd64 1.1.3-1 [5456 B]
3240s Get:8 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4ubuntu3 [1280 kB]
3240s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4ubuntu3 [56.6 kB]
3240s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB]
3240s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB]
3240s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblzf1 amd64 3.6-4 [7624 B]
3240s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB]
3240s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB]
3240s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B]
3240s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB]
3240s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py-serial amd64 3.11.0-5ubuntu1 [1107 kB]
3240s Get:18 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
3240s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-colorama all 0.4.6-4 [32.1 kB]
3240s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-click all 8.1.7-2 [79.5 kB]
3240s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-six all 1.16.0-7 [13.1 kB]
3240s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB]
3240s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-tz all 2024.1-2 [31.4 kB]
3240s Get:24 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas-lib amd64 2.2.3+dfsg-5 [5087 kB]
3241s Get:25 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
3241s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB]
3241s Get:27 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB]
3241s Get:28 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB]
3242s Fetched 43.5 MB in 2s (21.9 MB/s)
3242s Selecting previously unselected package libpython3.13-minimal:amd64.
3242s (Reading database ... 
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3242s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ...
3242s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ...
3242s Selecting previously unselected package python3.13-minimal.
3242s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ...
3242s Unpacking python3.13-minimal (3.13.0-2) ...
3242s Selecting previously unselected package libaec0:amd64.
3242s Preparing to unpack .../02-libaec0_1.1.3-1_amd64.deb ...
3242s Unpacking libaec0:amd64 (1.1.3-1) ...
3242s Selecting previously unselected package libblas3:amd64.
3242s Preparing to unpack .../03-libblas3_3.12.0-3build2_amd64.deb ...
3242s Unpacking libblas3:amd64 (3.12.0-3build2) ...
3242s Selecting previously unselected package libgfortran5:amd64.
3242s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_amd64.deb ...
3242s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ...
3242s Selecting previously unselected package libsz2:amd64.
3242s Preparing to unpack .../05-libsz2_1.1.3-1_amd64.deb ...
3242s Unpacking libsz2:amd64 (1.1.3-1) ...
3242s Selecting previously unselected package libhdf5-103-1t64:amd64.
3242s Preparing to unpack .../06-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_amd64.deb ...
3242s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
3242s Selecting previously unselected package libhdf5-hl-100t64:amd64.
3242s Preparing to unpack .../07-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_amd64.deb ...
3242s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ...
3242s Selecting previously unselected package liblapack3:amd64.
3242s Preparing to unpack .../08-liblapack3_3.12.0-3build2_amd64.deb ...
3242s Unpacking liblapack3:amd64 (3.12.0-3build2) ...
3242s Selecting previously unselected package liblbfgsb0:amd64.
3242s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ...
3242s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
3242s Selecting previously unselected package liblzf1:amd64.
3242s Preparing to unpack .../10-liblzf1_3.6-4_amd64.deb ...
3242s Unpacking liblzf1:amd64 (3.6-4) ...
3242s Selecting previously unselected package libpython3.13-stdlib:amd64.
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3242s Unpacking python3-all (3.12.7-1) ...
3242s Selecting previously unselected package python3-numpy.
3242s Preparing to unpack .../14-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ...
3242s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
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3242s Preparing to unpack .../15-python3-h5py-serial_3.11.0-5ubuntu1_amd64.deb ...
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3242s Preparing to unpack .../16-python3-h5py_3.11.0-5ubuntu1_all.deb ...
3242s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
3242s Selecting previously unselected package python3-colorama.
3242s Preparing to unpack .../17-python3-colorama_0.4.6-4_all.deb ...
3242s Unpacking python3-colorama (0.4.6-4) ...
3243s Selecting previously unselected package python3-click.
3243s Preparing to unpack .../18-python3-click_8.1.7-2_all.deb ...
3243s Unpacking python3-click (8.1.7-2) ...
3243s Selecting previously unselected package python3-six.
3243s Preparing to unpack .../19-python3-six_1.16.0-7_all.deb ...
3243s Unpacking python3-six (1.16.0-7) ...
3243s Selecting previously unselected package python3-dateutil.
3243s Preparing to unpack .../20-python3-dateutil_2.9.0-2_all.deb ...
3243s Unpacking python3-dateutil (2.9.0-2) ...
3243s Selecting previously unselected package python3-tz.
3243s Preparing to unpack .../21-python3-tz_2024.1-2_all.deb ...
3243s Unpacking python3-tz (2024.1-2) ...
3243s Selecting previously unselected package python3-pandas-lib:amd64.
3243s Preparing to unpack .../22-python3-pandas-lib_2.2.3+dfsg-5_amd64.deb ...
3243s Unpacking python3-pandas-lib:amd64 (2.2.3+dfsg-5) ...
3243s Selecting previously unselected package python3-pandas.
3243s Preparing to unpack .../23-python3-pandas_2.2.3+dfsg-5_all.deb ...
3243s Unpacking python3-pandas (2.2.3+dfsg-5) ...
3243s Selecting previously unselected package python3-decorator.
3243s Preparing to unpack .../24-python3-decorator_5.1.1-5_all.deb ...
3243s Unpacking python3-decorator (5.1.1-5) ...
3243s Selecting previously unselected package python3-scipy.
3243s Preparing to unpack .../25-python3-scipy_1.13.1-5_amd64.deb ...
3243s Unpacking python3-scipy (1.13.1-5) ...
3243s Selecting previously unselected package python3-biom-format.
3243s Preparing to unpack .../26-python3-biom-format_2.1.16-1_amd64.deb ...
3243s Unpacking python3-biom-format (2.1.16-1) ...
3243s Selecting previously unselected package autopkgtest-satdep.
3244s Preparing to unpack .../27-2-autopkgtest-satdep.deb ...
3244s Unpacking autopkgtest-satdep (0) ...
3244s Setting up python3-colorama (0.4.6-4) ...
3244s Setting up python3-click (8.1.7-2) ...
3244s Setting up libaec0:amd64 (1.1.3-1) ...
3244s Setting up python3-tz (2024.1-2) ...
3244s Setting up python3-six (1.16.0-7) ...
3244s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ...
3244s Setting up python3-decorator (5.1.1-5) ...
3244s Setting up libblas3:amd64 (3.12.0-3build2) ...
3244s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
3244s Setting up liblzf1:amd64 (3.6-4) ...
3244s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ...
3244s Setting up python3.13-minimal (3.13.0-2) ...
3245s Setting up python3-dateutil (2.9.0-2) ...
3245s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ...
3245s Setting up libsz2:amd64 (1.1.3-1) ...
3245s Setting up liblapack3:amd64 (3.12.0-3build2) ...
3245s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
3245s Setting up python3.13 (3.13.0-2) ...
3247s Setting up python3-all (3.12.7-1) ...
3247s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
3249s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4ubuntu3) ...
3249s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ...
3249s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4ubuntu3) ...
3249s Setting up python3-scipy (1.13.1-5) ...
3254s Setting up python3-pandas-lib:amd64 (2.2.3+dfsg-5) ...
3254s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
3255s Setting up python3-pandas (2.2.3+dfsg-5) ...
3262s Setting up python3-h5py (3.11.0-5ubuntu1) ...
3262s Setting up python3-biom-format (2.1.16-1) ...
3263s Setting up autopkgtest-satdep (0) ...
3263s Processing triggers for systemd (256.5-2ubuntu4) ...
3263s Processing triggers for man-db (2.12.1-3) ...
3263s Processing triggers for libc-bin (2.40-1ubuntu3) ...
3266s (Reading database ... 80697 files and directories currently installed.)
3266s Removing autopkgtest-satdep (0) ...
3282s autopkgtest [11:33:55]: 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
3282s autopkgtest [11:33:55]: test autodep8-python3: [-----------------------
3282s Testing with python3.13:
3282s Traceback (most recent call last):
3282s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
3282s     from . import multiarray
3282s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
3282s     from . import overrides
3282s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
3282s     from numpy.core._multiarray_umath import (
3282s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
3282s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
3282s 
3282s During handling of the above exception, another exception occurred:
3282s 
3282s Traceback (most recent call last):
3282s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
3282s     from numpy.__config__ import show as show_config
3282s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
3282s     from numpy.core._multiarray_umath import (
3282s     ...<3 lines>...
3282s     )
3282s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
3282s     raise ImportError(msg)
3282s ImportError: 
3282s 
3282s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
3282s 
3282s Importing the numpy C-extensions failed. This error can happen for
3282s many reasons, often due to issues with your setup or how NumPy was
3282s installed.
3282s 
3282s We have compiled some common reasons and troubleshooting tips at:
3282s 
3282s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
3282s 
3282s Please note and check the following:
3282s 
3282s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
3282s   * The NumPy version is: "1.26.4"
3282s 
3282s and make sure that they are the versions you expect.
3282s Please carefully study the documentation linked above for further help.
3282s 
3282s Original error was: No module named 'numpy.core._multiarray_umath'
3282s 
3282s 
3282s The above exception was the direct cause of the following exception:
3282s 
3282s Traceback (most recent call last):
3282s   File "<string>", line 1, in <module>
3282s     import biom; print(biom)
3282s     ^^^^^^^^^^^
3282s   File "/usr/lib/python3/dist-packages/biom/__init__.py", line 51, in <module>
3282s     from .table import Table
3282s   File "/usr/lib/python3/dist-packages/biom/table.py", line 174, in <module>
3282s     import numpy as np
3282s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
3282s     raise ImportError(msg) from e
3282s ImportError: Error importing numpy: you should not try to import numpy from
3282s         its source directory; please exit the numpy source tree, and relaunch
3282s         your python interpreter from there.
3283s autopkgtest [11:33:56]: test autodep8-python3: -----------------------]
3283s autopkgtest [11:33:56]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
3283s autodep8-python3     FAIL non-zero exit status 1
3283s autopkgtest [11:33:56]: @@@@@@@@@@@@@@@@@@@@ summary
3283s run-unit-test        PASS
3283s autodep8-python3     FAIL non-zero exit status 1
3467s nova [W] Skipping flock for amd64
3467s Creating nova instance adt-plucky-amd64-python-biom-format-20241113-103913-juju-7f2275-prod-proposed-migration-environment-15-bcfe9594-ab41-4f37-b684-45e4d8aed9b5 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...
3467s nova [W] Skipping flock for amd64
3467s Creating nova instance adt-plucky-amd64-python-biom-format-20241113-103913-juju-7f2275-prod-proposed-migration-environment-15-bcfe9594-ab41-4f37-b684-45e4d8aed9b5 from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...