0s autopkgtest [13:00:19]: starting date and time: 2024-11-13 13:00:19+0000
  0s autopkgtest [13:00:19]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [13:00:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3i966i1t/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 autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-14.secgroup --name adt-plucky-s390x-python-biom-format-20241113-130019-juju-7f2275-prod-proposed-migration-environment-15-c3bb24f3-0ff3-4a41-9553-11e09d634491 --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/
125s autopkgtest [13:02:24]: testbed dpkg architecture: s390x
125s autopkgtest [13:02:24]: testbed apt version: 2.9.8
125s autopkgtest [13:02:24]: @@@@@@@@@@@@@@@@@@@@ test bed setup
126s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
126s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
126s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB]
126s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB]
126s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
126s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB]
126s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB]
126s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB]
127s Fetched 1934 kB in 1s (2298 kB/s)
127s Reading package lists...
129s Reading package lists...
129s Building dependency tree...
129s Reading state information...
129s Calculating upgrade...
129s The following NEW packages will be installed:
129s   python3.13-gdbm
129s The following packages will be upgraded:
129s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
129s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
129s Need to get 252 kB of archives.
129s After this operation, 98.3 kB of additional disk space will be used.
129s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB]
129s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB]
129s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB]
129s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB]
129s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B]
129s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB]
130s Fetched 252 kB in 0s (628 kB/s)
130s (Reading database ... 
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(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 ... 55510 files and directories currently installed.)
130s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ...
130s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
130s Setting up python3-minimal (3.12.7-1) ...
130s (Reading database ... 
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(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 ... 55510 files and directories currently installed.)
130s Preparing to unpack .../python3_3.12.7-1_s390x.deb ...
130s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
130s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ...
130s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ...
130s Selecting previously unselected package python3.13-gdbm.
130s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ...
130s Unpacking python3.13-gdbm (3.13.0-2) ...
130s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ...
130s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ...
130s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ...
130s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
130s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ...
130s Setting up python3.13-gdbm (3.13.0-2) ...
130s Setting up libpython3-stdlib:s390x (3.12.7-1) ...
130s Setting up python3 (3.12.7-1) ...
130s Setting up python3-gdbm:s390x (3.12.7-1) ...
130s Processing triggers for man-db (2.12.1-3) ...
131s Processing triggers for libc-bin (2.40-1ubuntu3) ...
131s Reading package lists...
131s Building dependency tree...
131s Reading state information...
131s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
131s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
131s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
132s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
132s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
132s Reading package lists...
132s Reading package lists...
132s Building dependency tree...
132s Reading state information...
133s Calculating upgrade...
133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
133s Reading package lists...
133s Building dependency tree...
133s Reading state information...
133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
135s autopkgtest [13:02:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024
136s autopkgtest [13:02:35]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format
139s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B]
139s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB]
139s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB]
139s gpgv: Signature made Mon May 27 20:43:46 2024 UTC
139s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
139s gpgv:                issuer "emollier@debian.org"
139s gpgv: Can't check signature: No public key
139s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found
139s autopkgtest [13:02:38]: testing package python-biom-format version 2.1.16-1
140s autopkgtest [13:02:39]: build not needed
142s autopkgtest [13:02:41]: test run-unit-test: preparing testbed
146s Reading package lists...
146s Building dependency tree...
146s Reading state information...
147s Starting pkgProblemResolver with broken count: 0
147s Starting 2 pkgProblemResolver with broken count: 0
147s Done
147s The following additional packages will be installed:
147s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64
147s   libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
147s   libsz2 python-biom-format-doc python3-biom-format python3-click
147s   python3-colorama python3-dateutil python3-decorator python3-h5py
147s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
147s   python3-scipy python3-six python3-tz
147s Suggested packages:
147s   python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
147s   python-pandas-doc python3-statsmodels python-scipy-doc
147s Recommended packages:
147s   javascript-common python3-matplotlib python3-bottleneck python3-numexpr
147s   python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml
147s   python3-tables g++ | c++-compiler python3-pil
147s The following NEW packages will be installed:
147s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
147s   libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
147s   liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format
147s   python3-click python3-colorama python3-dateutil python3-decorator
147s   python3-h5py python3-h5py-serial python3-numpy python3-pandas
147s   python3-pandas-lib python3-scipy python3-six python3-tz
147s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
147s Need to get 37.2 MB/37.2 MB of archives.
147s After this operation, 160 MB of additional disk space will be used.
147s Get:1 /tmp/autopkgtest.LaAMH4/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [728 B]
147s Get:2 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB]
147s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB]
147s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB]
147s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B]
147s Get:6 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB]
147s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB]
147s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
147s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
147s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libjs-sphinxdoc all 7.4.7-4 [158 kB]
147s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB]
147s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB]
147s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B]
147s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x python-biom-format-doc all 2.1.16-1 [57.5 kB]
147s Get:15 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB]
148s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.11.0-5ubuntu1 [1151 kB]
148s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.11.0-5ubuntu1 [7974 B]
148s Get:18 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB]
148s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB]
148s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.16.0-7 [13.1 kB]
148s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-2 [80.3 kB]
148s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB]
148s Get:23 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5 [4938 kB]
149s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5 [3112 kB]
149s Get:25 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB]
149s Get:26 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB]
149s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1 [147 kB]
149s Fetched 37.2 MB in 3s (12.7 MB/s)
149s Selecting previously unselected package libaec0:s390x.
149s (Reading database ... 
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 55517 files and directories currently installed.)
149s Preparing to unpack .../00-libaec0_1.1.3-1_s390x.deb ...
149s Unpacking libaec0:s390x (1.1.3-1) ...
149s Selecting previously unselected package libblas3:s390x.
149s Preparing to unpack .../01-libblas3_3.12.0-3build2_s390x.deb ...
149s Unpacking libblas3:s390x (3.12.0-3build2) ...
149s Selecting previously unselected package libgfortran5:s390x.
149s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_s390x.deb ...
149s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ...
149s Selecting previously unselected package libsz2:s390x.
149s Preparing to unpack .../03-libsz2_1.1.3-1_s390x.deb ...
149s Unpacking libsz2:s390x (1.1.3-1) ...
149s Selecting previously unselected package libhdf5-103-1t64:s390x.
149s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_s390x.deb ...
149s Unpacking libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ...
149s Selecting previously unselected package libhdf5-hl-100t64:s390x.
149s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_s390x.deb ...
149s Unpacking libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ...
150s Selecting previously unselected package libjs-jquery.
150s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
150s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
150s Selecting previously unselected package libjs-underscore.
150s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
150s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
150s Selecting previously unselected package libjs-sphinxdoc.
150s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ...
150s Unpacking libjs-sphinxdoc (7.4.7-4) ...
150s Selecting previously unselected package liblapack3:s390x.
150s Preparing to unpack .../09-liblapack3_3.12.0-3build2_s390x.deb ...
150s Unpacking liblapack3:s390x (3.12.0-3build2) ...
150s Selecting previously unselected package liblbfgsb0:s390x.
150s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ...
150s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ...
150s Selecting previously unselected package liblzf1:s390x.
150s Preparing to unpack .../11-liblzf1_3.6-4_s390x.deb ...
150s Unpacking liblzf1:s390x (3.6-4) ...
150s Selecting previously unselected package python-biom-format-doc.
150s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ...
150s Unpacking python-biom-format-doc (2.1.16-1) ...
150s Selecting previously unselected package python3-numpy.
150s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ...
150s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
150s Selecting previously unselected package python3-h5py-serial.
150s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_s390x.deb ...
150s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
150s Selecting previously unselected package python3-h5py.
150s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ...
150s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
150s Selecting previously unselected package python3-colorama.
150s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ...
150s Unpacking python3-colorama (0.4.6-4) ...
150s Selecting previously unselected package python3-click.
150s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ...
150s Unpacking python3-click (8.1.7-2) ...
150s Selecting previously unselected package python3-six.
150s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ...
150s Unpacking python3-six (1.16.0-7) ...
150s Selecting previously unselected package python3-dateutil.
150s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ...
150s Unpacking python3-dateutil (2.9.0-2) ...
150s Selecting previously unselected package python3-tz.
150s Preparing to unpack .../20-python3-tz_2024.1-2_all.deb ...
150s Unpacking python3-tz (2024.1-2) ...
150s Selecting previously unselected package python3-pandas-lib:s390x.
150s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-5_s390x.deb ...
150s Unpacking python3-pandas-lib:s390x (2.2.3+dfsg-5) ...
150s Selecting previously unselected package python3-pandas.
150s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-5_all.deb ...
150s Unpacking python3-pandas (2.2.3+dfsg-5) ...
150s Selecting previously unselected package python3-decorator.
150s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ...
150s Unpacking python3-decorator (5.1.1-5) ...
150s Selecting previously unselected package python3-scipy.
150s Preparing to unpack .../24-python3-scipy_1.13.1-5_s390x.deb ...
150s Unpacking python3-scipy (1.13.1-5) ...
150s Selecting previously unselected package python3-biom-format.
150s Preparing to unpack .../25-python3-biom-format_2.1.16-1_s390x.deb ...
150s Unpacking python3-biom-format (2.1.16-1) ...
150s Selecting previously unselected package autopkgtest-satdep.
150s Preparing to unpack .../26-1-autopkgtest-satdep.deb ...
150s Unpacking autopkgtest-satdep (0) ...
151s Setting up python3-colorama (0.4.6-4) ...
151s Setting up python3-click (8.1.7-2) ...
151s Setting up libaec0:s390x (1.1.3-1) ...
151s Setting up python3-tz (2024.1-2) ...
151s Setting up python3-six (1.16.0-7) ...
151s Setting up python3-decorator (5.1.1-5) ...
151s Setting up libblas3:s390x (3.12.0-3build2) ...
151s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
151s Setting up liblzf1:s390x (3.6-4) ...
151s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ...
151s Setting up python3-dateutil (2.9.0-2) ...
151s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
151s Setting up libsz2:s390x (1.1.3-1) ...
151s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
151s Setting up liblapack3:s390x (3.12.0-3build2) ...
151s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
151s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
153s Setting up libjs-sphinxdoc (7.4.7-4) ...
153s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ...
153s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ...
153s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ...
153s Setting up python3-scipy (1.13.1-5) ...
157s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-5) ...
157s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
157s Setting up python-biom-format-doc (2.1.16-1) ...
157s Setting up python3-pandas (2.2.3+dfsg-5) ...
163s Setting up python3-h5py (3.11.0-5ubuntu1) ...
163s Setting up python3-biom-format (2.1.16-1) ...
163s Setting up autopkgtest-satdep (0) ...
163s Processing triggers for man-db (2.12.1-3) ...
163s Processing triggers for libc-bin (2.40-1ubuntu3) ...
165s (Reading database ... 60030 files and directories currently installed.)
165s Removing autopkgtest-satdep (0) ...
166s autopkgtest [13:03:05]: test run-unit-test: [-----------------------
167s 
167s System information
167s ==================
167s          Platform:	linux
167s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
167s Python executable:	/usr/bin/python3
167s 
167s Dependency versions
167s ===================
167s click version:	8.1.7
167s NumPy version:	1.26.4
167s SciPy version:	1.13.1
167s  h5py version:	3.11.0
167s 
167s biom-format package information
167s ===============================
167s biom-format version:	2.1.16
167s 
167s 
167s The input file is a valid BIOM-formatted file.
168s 
168s The input file is a valid BIOM-formatted file.
169s 
169s The input file is a valid BIOM-formatted file.
169s 
169s The input file is a valid BIOM-formatted file.
171s + table=examples/min_sparse_otu_table_hdf5.biom
171s + obsmd=examples/obs_md.txt
171s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
171s + biom show-install-info
171s 
171s System information
171s ==================
171s          Platform:	linux
171s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
171s Python executable:	/usr/bin/python3
171s 
171s Dependency versions
171s ===================
171s click version:	8.1.7
171s NumPy version:	1.26.4
171s SciPy version:	1.13.1
171s  h5py version:	3.11.0
171s 
171s biom-format package information
171s ===============================
171s biom-format version:	2.1.16
171s 
171s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
172s 
172s The input file is a valid BIOM-formatted file.
172s + 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
173s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json
173s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv
174s + biom validate-table -i test_json.biom
174s 
174s The input file is a valid BIOM-formatted file.
174s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
175s + biom validate-table -i test_hdf5.biom
176s 
176s The input file is a valid BIOM-formatted file.
176s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv
176s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table
177s + biom validate-table -i test_hdf5.biom
177s 
177s The input file is a valid BIOM-formatted file.
178s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table
178s + biom validate-table -i test_json.biom
179s 
179s The input file is a valid BIOM-formatted file.
179s + biom head -i examples/min_sparse_otu_table_hdf5.biom
179s # Constructed from biom file
179s #OTU ID	Sample1	Sample2	Sample3	Sample4	Sample5
179s GG_OTU_1	0.0	0.0	1.0	0.0	0.0
179s GG_OTU_2	5.0	1.0	0.0	2.0	3.0
179s GG_OTU_3	0.0	0.0	1.0	4.0	0.0
179s GG_OTU_4	2.0	1.0	1.0	0.0	0.0
179s GG_OTU_5	0.0	1.0	1.0	0.0	0.0
179s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
180s Sample1
180s Sample2
180s Sample3
180s Sample4
180s Sample5
180s Sample6
180s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p
181s + cat
181s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt
181s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
182s Num samples: 6
182s Num observations: 5
182s Total count: 27
182s Table density (fraction of non-zero values): 0.500
182s 
182s Counts/sample summary:
182s  Min: 3.000
182s  Max: 7.000
182s  Median: 4.000
182s  Mean: 4.500
182s  Std. dev.: 1.500
182s  Sample Metadata Categories: None provided
182s  Observation Metadata Categories: None provided
182s 
182s Counts/sample detail:
182s Sample2: 3.000
182s Sample5: 3.000
182s Sample3: 4.000
182s Sample6: 4.000
182s Sample4: 6.000
182s Sample1: 7.000
182s + cat
182s + biom from-uc -i uctest -o test_uc.biom
183s If this message was shown, then all commands executed without failure
183s + echo If this message was shown, then all commands executed without failure
183s autopkgtest [13:03:22]: test run-unit-test: -----------------------]
183s run-unit-test        PASS
183s autopkgtest [13:03:22]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
184s autopkgtest [13:03:23]: test autodep8-python3: preparing testbed
298s autopkgtest [13:05:17]: testbed dpkg architecture: s390x
298s autopkgtest [13:05:17]: testbed apt version: 2.9.8
298s autopkgtest [13:05:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup
299s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
299s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
299s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
299s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [967 kB]
299s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB]
299s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [107 kB]
299s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [641 kB]
299s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB]
300s Fetched 1934 kB in 1s (2254 kB/s)
300s Reading package lists...
302s Reading package lists...
302s Building dependency tree...
302s Reading state information...
302s Calculating upgrade...
302s The following NEW packages will be installed:
302s   python3.13-gdbm
302s The following packages will be upgraded:
302s   libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal
302s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
302s Need to get 252 kB of archives.
302s After this operation, 98.3 kB of additional disk space will be used.
302s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB]
302s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB]
302s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB]
302s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB]
302s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B]
302s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB]
303s Fetched 252 kB in 0s (565 kB/s)
303s (Reading database ... 
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303s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ...
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303s Setting up python3-minimal (3.12.7-1) ...
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303s Preparing to unpack .../python3_3.12.7-1_s390x.deb ...
303s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
303s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ...
303s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ...
303s Selecting previously unselected package python3.13-gdbm.
303s Preparing to unpack .../python3.13-gdbm_3.13.0-2_s390x.deb ...
303s Unpacking python3.13-gdbm (3.13.0-2) ...
303s Preparing to unpack .../python3-gdbm_3.12.7-1_s390x.deb ...
303s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ...
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303s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ...
303s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ...
303s Setting up python3.13-gdbm (3.13.0-2) ...
303s Setting up libpython3-stdlib:s390x (3.12.7-1) ...
303s Setting up python3 (3.12.7-1) ...
303s Setting up python3-gdbm:s390x (3.12.7-1) ...
303s Processing triggers for man-db (2.12.1-3) ...
304s Processing triggers for libc-bin (2.40-1ubuntu3) ...
304s Reading package lists...
304s Building dependency tree...
304s Reading state information...
304s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
305s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
305s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
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306s Reading package lists...
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311s Reading package lists...
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311s Starting pkgProblemResolver with broken count: 0
311s Starting 2 pkgProblemResolver with broken count: 0
311s Done
311s The following additional packages will be installed:
311s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3
311s   liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2
311s   python3-all python3-biom-format python3-click python3-colorama
311s   python3-dateutil python3-decorator python3-h5py python3-h5py-serial
311s   python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-six
311s   python3-tz python3.13 python3.13-minimal
311s Suggested packages:
311s   python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc
311s   python3-dev python3-pytest python-pandas-doc python3-statsmodels
311s   python-scipy-doc python3.13-venv python3.13-doc binfmt-support
311s Recommended packages:
311s   python3-matplotlib python3-bottleneck python3-numexpr python3-odf
311s   python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables
311s   g++ | c++-compiler python3-pil
311s The following NEW packages will be installed:
311s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
311s   libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal
311s   libpython3.13-stdlib libsz2 python3-all python3-biom-format python3-click
311s   python3-colorama python3-dateutil python3-decorator python3-h5py
311s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
311s   python3-scipy python3-six python3-tz python3.13 python3.13-minimal
311s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
311s Need to get 42.4 MB/42.4 MB of archives.
311s After this operation, 180 MB of additional disk space will be used.
311s Get:1 /tmp/autopkgtest.LaAMH4/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [724 B]
311s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB]
312s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB]
312s Get:4 http://ftpmaster.internal/ubuntu plucky/universe s390x libaec0 s390x 1.1.3-1 [25.7 kB]
312s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB]
312s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB]
312s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x libsz2 s390x 1.1.3-1 [5442 B]
312s Get:8 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-103-1t64 s390x 1.10.10+repack-4ubuntu3 [1426 kB]
312s Get:9 http://ftpmaster.internal/ubuntu plucky/universe s390x libhdf5-hl-100t64 s390x 1.10.10+repack-4ubuntu3 [58.0 kB]
312s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB]
312s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB]
312s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x liblzf1 s390x 3.6-4 [7020 B]
312s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB]
312s Get:14 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB]
312s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B]
312s Get:16 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB]
312s Get:17 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py-serial s390x 3.11.0-5ubuntu1 [1151 kB]
312s Get:18 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-h5py all 3.11.0-5ubuntu1 [7974 B]
312s Get:19 http://ftpmaster.internal/ubuntu plucky/main s390x python3-colorama all 0.4.6-4 [32.1 kB]
312s Get:20 http://ftpmaster.internal/ubuntu plucky/main s390x python3-click all 8.1.7-2 [79.5 kB]
312s Get:21 http://ftpmaster.internal/ubuntu plucky/main s390x python3-six all 1.16.0-7 [13.1 kB]
312s Get:22 http://ftpmaster.internal/ubuntu plucky/main s390x python3-dateutil all 2.9.0-2 [80.3 kB]
312s Get:23 http://ftpmaster.internal/ubuntu plucky/main s390x python3-tz all 2024.1-2 [31.4 kB]
312s Get:24 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas-lib s390x 2.2.3+dfsg-5 [4938 kB]
313s Get:25 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pandas all 2.2.3+dfsg-5 [3112 kB]
313s Get:26 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB]
313s Get:27 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB]
313s Get:28 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-biom-format s390x 2.1.16-1 [147 kB]
313s Fetched 42.4 MB in 2s (22.2 MB/s)
313s Selecting previously unselected package libpython3.13-minimal:s390x.
313s (Reading database ... 
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314s Preparing to unpack .../08-liblapack3_3.12.0-3build2_s390x.deb ...
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314s Unpacking python3-six (1.16.0-7) ...
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314s Selecting previously unselected package python3-tz.
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315s Preparing to unpack .../27-2-autopkgtest-satdep.deb ...
315s Unpacking autopkgtest-satdep (0) ...
315s Setting up python3-colorama (0.4.6-4) ...
315s Setting up python3-click (8.1.7-2) ...
315s Setting up libaec0:s390x (1.1.3-1) ...
315s Setting up python3-tz (2024.1-2) ...
315s Setting up python3-six (1.16.0-7) ...
315s Setting up libpython3.13-minimal:s390x (3.13.0-2) ...
315s Setting up python3-decorator (5.1.1-5) ...
316s Setting up libblas3:s390x (3.12.0-3build2) ...
316s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode
316s Setting up liblzf1:s390x (3.6-4) ...
316s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ...
316s Setting up python3.13-minimal (3.13.0-2) ...
316s Setting up python3-dateutil (2.9.0-2) ...
317s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ...
317s Setting up libsz2:s390x (1.1.3-1) ...
317s Setting up liblapack3:s390x (3.12.0-3build2) ...
317s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode
317s Setting up python3.13 (3.13.0-2) ...
318s Setting up python3-all (3.12.7-1) ...
318s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
322s Setting up libhdf5-103-1t64:s390x (1.10.10+repack-4ubuntu3) ...
322s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ...
322s Setting up libhdf5-hl-100t64:s390x (1.10.10+repack-4ubuntu3) ...
322s Setting up python3-scipy (1.13.1-5) ...
331s Setting up python3-pandas-lib:s390x (2.2.3+dfsg-5) ...
331s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
331s Setting up python3-pandas (2.2.3+dfsg-5) ...
343s Setting up python3-h5py (3.11.0-5ubuntu1) ...
343s Setting up python3-biom-format (2.1.16-1) ...
344s Setting up autopkgtest-satdep (0) ...
344s Processing triggers for systemd (256.5-2ubuntu4) ...
344s Processing triggers for man-db (2.12.1-3) ...
344s Processing triggers for libc-bin (2.40-1ubuntu3) ...
346s (Reading database ... 60666 files and directories currently installed.)
346s Removing autopkgtest-satdep (0) ...
350s autopkgtest [13:06:09]: 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
350s autopkgtest [13:06:09]: test autodep8-python3: [-----------------------
350s Testing with python3.13:
350s Traceback (most recent call last):
350s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
350s     from . import multiarray
350s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
350s     from . import overrides
350s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
350s     from numpy.core._multiarray_umath import (
350s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
350s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
350s 
350s During handling of the above exception, another exception occurred:
350s 
350s Traceback (most recent call last):
350s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
350s     from numpy.__config__ import show as show_config
350s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
350s     from numpy.core._multiarray_umath import (
350s     ...<3 lines>...
350s     )
350s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
350s     raise ImportError(msg)
350s ImportError: 
350s 
350s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
350s 
350s Importing the numpy C-extensions failed. This error can happen for
350s many reasons, often due to issues with your setup or how NumPy was
350s installed.
350s 
350s We have compiled some common reasons and troubleshooting tips at:
350s 
350s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
350s 
350s Please note and check the following:
350s 
350s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
350s   * The NumPy version is: "1.26.4"
350s 
350s and make sure that they are the versions you expect.
350s Please carefully study the documentation linked above for further help.
350s 
350s Original error was: No module named 'numpy.core._multiarray_umath'
350s 
350s 
350s The above exception was the direct cause of the following exception:
350s 
350s Traceback (most recent call last):
350s   File "<string>", line 1, in <module>
350s     import biom; print(biom)
350s     ^^^^^^^^^^^
350s   File "/usr/lib/python3/dist-packages/biom/__init__.py", line 51, in <module>
350s     from .table import Table
350s   File "/usr/lib/python3/dist-packages/biom/table.py", line 174, in <module>
350s     import numpy as np
350s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
350s     raise ImportError(msg) from e
350s ImportError: Error importing numpy: you should not try to import numpy from
350s         its source directory; please exit the numpy source tree, and relaunch
350s         your python interpreter from there.
350s autopkgtest [13:06:09]: test autodep8-python3: -----------------------]
351s autodep8-python3     FAIL non-zero exit status 1
351s autopkgtest [13:06:10]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
351s autopkgtest [13:06:10]: @@@@@@@@@@@@@@@@@@@@ summary
351s run-unit-test        PASS
351s autodep8-python3     FAIL non-zero exit status 1
357s nova [W] Using flock in prodstack6-s390x
357s Creating nova instance adt-plucky-s390x-python-biom-format-20241113-130019-juju-7f2275-prod-proposed-migration-environment-15-c3bb24f3-0ff3-4a41-9553-11e09d634491 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...
357s nova [W] Using flock in prodstack6-s390x
357s flock: timeout while waiting to get lock
357s Creating nova instance adt-plucky-s390x-python-biom-format-20241113-130019-juju-7f2275-prod-proposed-migration-environment-15-c3bb24f3-0ff3-4a41-9553-11e09d634491 from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...