0s autopkgtest [21:18:08]: starting date and time: 2024-11-13 21:18:08+0000
  0s autopkgtest [21:18:08]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [21:18:08]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.57ne46nt/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-23.secgroup --name adt-plucky-ppc64el-python-biom-format-20241113-211808-juju-7f2275-prod-proposed-migration-environment-15-76de6dfe-f1de-4c77-941c-7aaa02341df4 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/
111s autopkgtest [21:19:59]: testbed dpkg architecture: ppc64el
111s autopkgtest [21:19:59]: testbed apt version: 2.9.8
111s autopkgtest [21:19:59]: @@@@@@@@@@@@@@@@@@@@ test bed setup
112s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
112s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB]
112s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
112s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
112s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
112s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB]
112s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [679 kB]
112s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB]
113s Fetched 1978 kB in 1s (2081 kB/s)
113s Reading package lists...
115s Reading package lists...
116s Building dependency tree...
116s Reading state information...
116s Calculating upgrade...
116s The following NEW packages will be installed:
116s   python3.13-gdbm
116s The following packages will be upgraded:
116s   bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0
116s   libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3
116s   python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail
116s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
116s Need to get 4700 kB of archives.
116s After this operation, 215 kB of additional disk space will be used.
116s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
116s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
116s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
116s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
117s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
117s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
117s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
117s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
117s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
117s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
117s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
117s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
117s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
117s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
117s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
117s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
117s Fetched 4700 kB in 1s (5947 kB/s)
118s (Reading database ... 
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(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
118s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
118s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
118s Setting up python3-minimal (3.12.7-1) ...
118s (Reading database ... 
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(Reading database ... 70%
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(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
118s Preparing to unpack .../python3_3.12.7-1_ppc64el.deb ...
118s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
118s Preparing to unpack .../libpython3-stdlib_3.12.7-1_ppc64el.deb ...
118s Unpacking libpython3-stdlib:ppc64el (3.12.7-1) over (3.12.6-0ubuntu1) ...
118s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ...
118s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
118s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ...
118s (Reading database ... 
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(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 73767 files and directories currently installed.)
118s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ...
118s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
118s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ...
118s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
118s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ...
118s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
118s Selecting previously unselected package python3.13-gdbm.
118s Preparing to unpack .../03-python3.13-gdbm_3.13.0-2_ppc64el.deb ...
118s Unpacking python3.13-gdbm (3.13.0-2) ...
118s Preparing to unpack .../04-python3-gdbm_3.12.7-1_ppc64el.deb ...
118s Unpacking python3-gdbm:ppc64el (3.12.7-1) over (3.12.6-1ubuntu1) ...
118s Preparing to unpack .../05-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ...
118s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
118s Preparing to unpack .../06-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ...
118s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
118s Preparing to unpack .../07-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ...
118s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
119s Preparing to unpack .../08-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ...
119s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ...
119s Preparing to unpack .../09-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
119s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
119s Preparing to unpack .../10-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ...
119s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ...
119s Preparing to unpack .../11-libutempter0_1.2.1-4_ppc64el.deb ...
119s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ...
119s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ...
119s Setting up libutempter0:ppc64el (1.2.1-4) ...
119s Setting up whiptail (0.52.24-2ubuntu4) ...
119s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
119s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
119s Setting up python3.13-gdbm (3.13.0-2) ...
119s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
119s Setting up bpftrace (0.21.2-2ubuntu2) ...
119s Setting up python3 (3.12.7-1) ...
119s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
120s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
120s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
120s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
120s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
120s Processing triggers for man-db (2.12.1-3) ...
121s Processing triggers for libc-bin (2.40-1ubuntu3) ...
121s Reading package lists...
122s Building dependency tree...
122s Reading state information...
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
123s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
123s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
123s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
123s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
124s Reading package lists...
124s Reading package lists...
124s Building dependency tree...
124s Reading state information...
124s Calculating upgrade...
125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
125s Reading package lists...
125s Building dependency tree...
125s Reading state information...
125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
128s autopkgtest [21:20:16]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
128s autopkgtest [21:20:16]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format
131s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B]
131s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB]
131s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB]
131s gpgv: Signature made Mon May 27 20:43:46 2024 UTC
131s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
131s gpgv:                issuer "emollier@debian.org"
131s gpgv: Can't check signature: No public key
131s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found
132s autopkgtest [21:20:20]: testing package python-biom-format version 2.1.16-1
133s autopkgtest [21:20:21]: build not needed
135s autopkgtest [21:20:23]: test run-unit-test: preparing testbed
140s Reading package lists...
140s Building dependency tree...
140s Reading state information...
140s Starting pkgProblemResolver with broken count: 0
140s Starting 2 pkgProblemResolver with broken count: 0
140s Done
140s The following additional packages will be installed:
140s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64
140s   libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
140s   libsz2 python-biom-format-doc python3-biom-format python3-click
140s   python3-colorama python3-dateutil python3-decorator python3-h5py
140s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
140s   python3-scipy python3-six python3-tz
140s Suggested packages:
140s   python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
140s   python-pandas-doc python3-statsmodels python-scipy-doc
140s Recommended packages:
140s   javascript-common python3-matplotlib python3-bottleneck python3-numexpr
140s   python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml
140s   python3-tables g++ | c++-compiler python3-pil
140s The following NEW packages will be installed:
140s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
140s   libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
140s   liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format
140s   python3-click python3-colorama python3-dateutil python3-decorator
140s   python3-h5py python3-h5py-serial python3-numpy python3-pandas
140s   python3-pandas-lib python3-scipy python3-six python3-tz
141s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
141s Need to get 38.0 MB/38.0 MB of archives.
141s After this operation, 181 MB of additional disk space will be used.
141s Get:1 /tmp/autopkgtest.cGEvaL/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
141s Get:2 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB]
141s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
141s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
141s Get:5 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B]
141s Get:6 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB]
141s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB]
141s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
141s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
141s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB]
141s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
141s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB]
141s Get:13 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B]
141s Get:14 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-biom-format-doc all 2.1.16-1 [57.5 kB]
141s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
141s Get:16 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB]
141s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B]
141s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB]
141s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-click all 8.1.7-2 [79.5 kB]
141s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB]
141s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB]
141s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB]
141s Get:23 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB]
142s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB]
142s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
142s Get:26 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB]
142s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biom-format ppc64el 2.1.16-1 [152 kB]
142s Fetched 38.0 MB in 2s (24.6 MB/s)
142s Selecting previously unselected package libaec0:ppc64el.
142s (Reading database ... 
(Reading database ... 5%
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(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 ... 73775 files and directories currently installed.)
142s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ...
142s Unpacking libaec0:ppc64el (1.1.3-1) ...
142s Selecting previously unselected package libblas3:ppc64el.
142s Preparing to unpack .../01-libblas3_3.12.0-3build2_ppc64el.deb ...
142s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
143s Selecting previously unselected package libgfortran5:ppc64el.
143s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ...
143s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
143s Selecting previously unselected package libsz2:ppc64el.
143s Preparing to unpack .../03-libsz2_1.1.3-1_ppc64el.deb ...
143s Unpacking libsz2:ppc64el (1.1.3-1) ...
143s Selecting previously unselected package libhdf5-103-1t64:ppc64el.
143s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ...
143s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
143s Selecting previously unselected package libhdf5-hl-100t64:ppc64el.
143s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ...
143s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ...
143s Selecting previously unselected package libjs-jquery.
143s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
143s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
143s Selecting previously unselected package libjs-underscore.
143s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
143s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
143s Selecting previously unselected package libjs-sphinxdoc.
143s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ...
143s Unpacking libjs-sphinxdoc (7.4.7-4) ...
143s Selecting previously unselected package liblapack3:ppc64el.
143s Preparing to unpack .../09-liblapack3_3.12.0-3build2_ppc64el.deb ...
143s Unpacking liblapack3:ppc64el (3.12.0-3build2) ...
143s Selecting previously unselected package liblbfgsb0:ppc64el.
143s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ...
143s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
143s Selecting previously unselected package liblzf1:ppc64el.
143s Preparing to unpack .../11-liblzf1_3.6-4_ppc64el.deb ...
143s Unpacking liblzf1:ppc64el (3.6-4) ...
143s Selecting previously unselected package python-biom-format-doc.
143s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ...
143s Unpacking python-biom-format-doc (2.1.16-1) ...
143s Selecting previously unselected package python3-numpy.
143s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_ppc64el.deb ...
143s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
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143s Selecting previously unselected package python3-six.
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143s Unpacking python3-six (1.16.0-7) ...
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144s Selecting previously unselected package python3-pandas.
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144s Unpacking python3-pandas (2.2.3+dfsg-5) ...
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145s Setting up python3-colorama (0.4.6-4) ...
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145s Setting up libaec0:ppc64el (1.1.3-1) ...
145s Setting up python3-tz (2024.1-2) ...
145s Setting up python3-six (1.16.0-7) ...
145s Setting up python3-decorator (5.1.1-5) ...
145s Setting up libblas3:ppc64el (3.12.0-3build2) ...
145s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
145s Setting up liblzf1:ppc64el (3.6-4) ...
145s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
145s Setting up python3-dateutil (2.9.0-2) ...
146s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
146s Setting up libsz2:ppc64el (1.1.3-1) ...
146s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
146s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
146s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
146s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
148s Setting up libjs-sphinxdoc (7.4.7-4) ...
148s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
148s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
148s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ...
148s Setting up python3-scipy (1.13.1-5) ...
153s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ...
153s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
153s Setting up python-biom-format-doc (2.1.16-1) ...
153s Setting up python3-pandas (2.2.3+dfsg-5) ...
160s Setting up python3-h5py (3.11.0-5ubuntu1) ...
160s Setting up python3-biom-format (2.1.16-1) ...
160s Setting up autopkgtest-satdep (0) ...
160s Processing triggers for man-db (2.12.1-3) ...
161s Processing triggers for libc-bin (2.40-1ubuntu3) ...
164s (Reading database ... 78288 files and directories currently installed.)
164s Removing autopkgtest-satdep (0) ...
164s autopkgtest [21:20:52]: test run-unit-test: [-----------------------
166s 
166s System information
166s ==================
166s          Platform:	linux
166s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
166s Python executable:	/usr/bin/python3
166s 
166s Dependency versions
166s ===================
166s click version:	8.1.7
166s NumPy version:	1.26.4
166s SciPy version:	1.13.1
166s  h5py version:	3.11.0
166s 
166s biom-format package information
166s ===============================
166s biom-format version:	2.1.16
166s 
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.
170s 
170s The input file is a valid BIOM-formatted file.
172s + table=examples/min_sparse_otu_table_hdf5.biom
172s + obsmd=examples/obs_md.txt
172s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
172s + biom show-install-info
173s 
173s System information
173s ==================
173s          Platform:	linux
173s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
173s Python executable:	/usr/bin/python3
173s 
173s Dependency versions
173s ===================
173s click version:	8.1.7
173s NumPy version:	1.26.4
173s SciPy version:	1.13.1
173s  h5py version:	3.11.0
173s 
173s biom-format package information
173s ===============================
173s biom-format version:	2.1.16
173s 
173s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
174s 
174s The input file is a valid BIOM-formatted file.
174s + 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
175s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json
176s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv
177s + biom validate-table -i test_json.biom
178s 
178s The input file is a valid BIOM-formatted file.
178s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
179s + biom validate-table -i test_hdf5.biom
179s 
179s The input file is a valid BIOM-formatted file.
180s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv
181s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table
182s + biom validate-table -i test_hdf5.biom
183s 
183s The input file is a valid BIOM-formatted file.
183s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table
184s + biom validate-table -i test_json.biom
184s 
184s The input file is a valid BIOM-formatted file.
185s + biom head -i examples/min_sparse_otu_table_hdf5.biom
185s # Constructed from biom file
185s #OTU ID	Sample1	Sample2	Sample3	Sample4	Sample5
185s GG_OTU_1	0.0	0.0	1.0	0.0	0.0
185s GG_OTU_2	5.0	1.0	0.0	2.0	3.0
185s GG_OTU_3	0.0	0.0	1.0	4.0	0.0
185s GG_OTU_4	2.0	1.0	1.0	0.0	0.0
185s GG_OTU_5	0.0	1.0	1.0	0.0	0.0
186s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
187s Sample1
187s Sample2
187s Sample3
187s Sample4
187s Sample5
187s Sample6
187s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p
188s + cat
188s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt
189s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
189s Num samples: 6
189s Num observations: 5
189s Total count: 27
189s Table density (fraction of non-zero values): 0.500
189s 
189s Counts/sample summary:
189s  Min: 3.000
189s  Max: 7.000
189s  Median: 4.000
189s  Mean: 4.500
189s  Std. dev.: 1.500
189s  Sample Metadata Categories: None provided
189s  Observation Metadata Categories: None provided
189s 
189s Counts/sample detail:
189s Sample2: 3.000
189s Sample5: 3.000
189s Sample3: 4.000
189s Sample6: 4.000
189s Sample4: 6.000
189s Sample1: 7.000
190s + cat
190s + biom from-uc -i uctest -o test_uc.biom
191s If this message was shown, then all commands executed without failure
191s + echo If this message was shown, then all commands executed without failure
191s autopkgtest [21:21:19]: test run-unit-test: -----------------------]
191s run-unit-test        PASS
191s autopkgtest [21:21:19]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
192s autopkgtest [21:21:20]: test autodep8-python3: preparing testbed
300s autopkgtest [21:23:08]: testbed dpkg architecture: ppc64el
300s autopkgtest [21:23:08]: testbed apt version: 2.9.8
300s autopkgtest [21:23:08]: @@@@@@@@@@@@@@@@@@@@ test bed setup
301s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
301s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
301s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB]
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301s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB]
301s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [110 kB]
301s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [679 kB]
301s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [20.8 kB]
302s Fetched 1978 kB in 1s (2054 kB/s)
302s Reading package lists...
304s Reading package lists...
304s Building dependency tree...
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304s Calculating upgrade...
305s The following NEW packages will be installed:
305s   python3.13-gdbm
305s The following packages will be upgraded:
305s   bpfcc-tools bpftrace libbpfcc libgnutls30t64 libjson-glib-1.0-0
305s   libjson-glib-1.0-common libnewt0.52 libpython3-stdlib libutempter0 python3
305s   python3-bpfcc python3-gdbm python3-minimal python3-newt whiptail
305s 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
305s Need to get 4700 kB of archives.
305s After this operation, 215 kB of additional disk space will be used.
305s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-minimal ppc64el 3.12.7-1 [27.4 kB]
305s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3 ppc64el 3.12.7-1 [24.0 kB]
305s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el libpython3-stdlib ppc64el 3.12.7-1 [10.0 kB]
305s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
305s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
305s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
305s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
305s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-gdbm ppc64el 3.13.0-2 [31.5 kB]
305s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-gdbm ppc64el 3.12.7-1 [8640 B]
305s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
305s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
305s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
305s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
305s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
305s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
305s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
306s Fetched 4700 kB in 1s (5444 kB/s)
306s (Reading database ... 
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306s Preparing to unpack .../python3-minimal_3.12.7-1_ppc64el.deb ...
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307s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
307s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
307s Setting up python3.13-gdbm (3.13.0-2) ...
307s Setting up libpython3-stdlib:ppc64el (3.12.7-1) ...
307s Setting up bpftrace (0.21.2-2ubuntu2) ...
307s Setting up python3 (3.12.7-1) ...
307s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
308s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
308s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
308s Setting up python3-gdbm:ppc64el (3.12.7-1) ...
308s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
308s Processing triggers for man-db (2.12.1-3) ...
309s Processing triggers for libc-bin (2.40-1ubuntu3) ...
309s Reading package lists...
310s Building dependency tree...
310s Reading state information...
310s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
311s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
311s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
311s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
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312s Reading package lists...
312s Reading package lists...
312s Building dependency tree...
312s Reading state information...
312s Calculating upgrade...
312s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
312s Reading package lists...
313s Building dependency tree...
313s Reading state information...
313s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
318s Reading package lists...
318s Building dependency tree...
318s Reading state information...
318s Starting pkgProblemResolver with broken count: 0
318s Starting 2 pkgProblemResolver with broken count: 0
318s Done
319s The following additional packages will be installed:
319s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3
319s   liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2
319s   python3-all python3-biom-format python3-click python3-colorama
319s   python3-dateutil python3-decorator python3-h5py python3-h5py-serial
319s   python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-six
319s   python3-tz python3.13 python3.13-minimal
319s Suggested packages:
319s   python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc
319s   python3-dev python3-pytest python-pandas-doc python3-statsmodels
319s   python-scipy-doc python3.13-venv python3.13-doc binfmt-support
319s Recommended packages:
319s   python3-matplotlib python3-bottleneck python3-numexpr python3-odf
319s   python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables
319s   g++ | c++-compiler python3-pil
319s The following NEW packages will be installed:
319s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
319s   libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal
319s   libpython3.13-stdlib libsz2 python3-all python3-biom-format python3-click
319s   python3-colorama python3-dateutil python3-decorator python3-h5py
319s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
319s   python3-scipy python3-six python3-tz python3.13 python3.13-minimal
319s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
319s Need to get 43.4 MB/43.4 MB of archives.
319s After this operation, 205 MB of additional disk space will be used.
319s Get:1 /tmp/autopkgtest.cGEvaL/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [724 B]
319s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-minimal ppc64el 3.13.0-2 [881 kB]
320s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13-minimal ppc64el 3.13.0-2 [2302 kB]
320s Get:4 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB]
320s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
320s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
321s Get:7 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B]
321s Get:8 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB]
321s Get:9 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB]
321s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
321s Get:11 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB]
321s Get:12 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B]
321s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.13-stdlib ppc64el 3.13.0-2 [2148 kB]
321s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.13 ppc64el 3.13.0-2 [719 kB]
322s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-all ppc64el 3.12.7-1 [888 B]
322s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11build1 [4434 kB]
322s Get:17 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB]
322s Get:18 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B]
322s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB]
322s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-click all 8.1.7-2 [79.5 kB]
322s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB]
322s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB]
322s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB]
322s Get:24 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB]
322s Get:25 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB]
323s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
323s Get:27 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB]
323s Get:28 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biom-format ppc64el 2.1.16-1 [152 kB]
324s Fetched 43.4 MB in 5s (9605 kB/s)
324s Selecting previously unselected package libpython3.13-minimal:ppc64el.
324s (Reading database ... 
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324s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_ppc64el.deb ...
324s Unpacking libpython3.13-minimal:ppc64el (3.13.0-2) ...
324s Selecting previously unselected package python3.13-minimal.
324s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_ppc64el.deb ...
324s Unpacking python3.13-minimal (3.13.0-2) ...
324s Selecting previously unselected package libaec0:ppc64el.
324s Preparing to unpack .../02-libaec0_1.1.3-1_ppc64el.deb ...
324s Unpacking libaec0:ppc64el (1.1.3-1) ...
324s Selecting previously unselected package libblas3:ppc64el.
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324s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
324s Selecting previously unselected package libgfortran5:ppc64el.
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324s Selecting previously unselected package libsz2:ppc64el.
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324s Selecting previously unselected package python3-numpy.
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325s Selecting previously unselected package python3-h5py-serial.
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325s Selecting previously unselected package python3-h5py.
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325s Selecting previously unselected package python3-colorama.
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325s Unpacking python3-colorama (0.4.6-4) ...
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325s Preparing to unpack .../18-python3-click_8.1.7-2_all.deb ...
325s Unpacking python3-click (8.1.7-2) ...
325s Selecting previously unselected package python3-six.
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325s Selecting previously unselected package python3-dateutil.
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325s Selecting previously unselected package python3-pandas-lib:ppc64el.
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325s Unpacking python3-scipy (1.13.1-5) ...
326s Selecting previously unselected package python3-biom-format.
326s Preparing to unpack .../26-python3-biom-format_2.1.16-1_ppc64el.deb ...
326s Unpacking python3-biom-format (2.1.16-1) ...
326s Selecting previously unselected package autopkgtest-satdep.
326s Preparing to unpack .../27-2-autopkgtest-satdep.deb ...
326s Unpacking autopkgtest-satdep (0) ...
326s Setting up python3-colorama (0.4.6-4) ...
326s Setting up python3-click (8.1.7-2) ...
326s Setting up libaec0:ppc64el (1.1.3-1) ...
326s Setting up python3-tz (2024.1-2) ...
327s Setting up python3-six (1.16.0-7) ...
327s Setting up libpython3.13-minimal:ppc64el (3.13.0-2) ...
327s Setting up python3-decorator (5.1.1-5) ...
327s Setting up libblas3:ppc64el (3.12.0-3build2) ...
327s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode
327s Setting up liblzf1:ppc64el (3.6-4) ...
327s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
327s Setting up python3.13-minimal (3.13.0-2) ...
328s Setting up python3-dateutil (2.9.0-2) ...
328s Setting up libpython3.13-stdlib:ppc64el (3.13.0-2) ...
328s Setting up libsz2:ppc64el (1.1.3-1) ...
328s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
328s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode
328s Setting up python3.13 (3.13.0-2) ...
330s Setting up python3-all (3.12.7-1) ...
330s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
334s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
334s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
334s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ...
334s Setting up python3-scipy (1.13.1-5) ...
343s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ...
343s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
343s Setting up python3-pandas (2.2.3+dfsg-5) ...
356s Setting up python3-h5py (3.11.0-5ubuntu1) ...
356s Setting up python3-biom-format (2.1.16-1) ...
356s Setting up autopkgtest-satdep (0) ...
356s Processing triggers for systemd (256.5-2ubuntu4) ...
356s Processing triggers for man-db (2.12.1-3) ...
356s Processing triggers for libc-bin (2.40-1ubuntu3) ...
359s (Reading database ... 78924 files and directories currently installed.)
359s Removing autopkgtest-satdep (0) ...
365s autopkgtest [21:24:13]: 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
365s autopkgtest [21:24:13]: test autodep8-python3: [-----------------------
366s Testing with python3.13:
366s Traceback (most recent call last):
366s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
366s     from . import multiarray
366s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
366s     from . import overrides
366s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
366s     from numpy.core._multiarray_umath import (
366s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
366s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
366s 
366s During handling of the above exception, another exception occurred:
366s 
366s Traceback (most recent call last):
366s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
366s     from numpy.__config__ import show as show_config
366s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
366s     from numpy.core._multiarray_umath import (
366s     ...<3 lines>...
366s     )
366s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
366s     raise ImportError(msg)
366s ImportError: 
366s 
366s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
366s 
366s Importing the numpy C-extensions failed. This error can happen for
366s many reasons, often due to issues with your setup or how NumPy was
366s installed.
366s 
366s We have compiled some common reasons and troubleshooting tips at:
366s 
366s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
366s 
366s Please note and check the following:
366s 
366s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
366s   * The NumPy version is: "1.26.4"
366s 
366s and make sure that they are the versions you expect.
366s Please carefully study the documentation linked above for further help.
366s 
366s Original error was: No module named 'numpy.core._multiarray_umath'
366s 
366s 
366s The above exception was the direct cause of the following exception:
366s 
366s Traceback (most recent call last):
366s   File "<string>", line 1, in <module>
366s     import biom; print(biom)
366s     ^^^^^^^^^^^
366s   File "/usr/lib/python3/dist-packages/biom/__init__.py", line 51, in <module>
366s     from .table import Table
366s   File "/usr/lib/python3/dist-packages/biom/table.py", line 174, in <module>
366s     import numpy as np
366s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
366s     raise ImportError(msg) from e
366s ImportError: Error importing numpy: you should not try to import numpy from
366s         its source directory; please exit the numpy source tree, and relaunch
366s         your python interpreter from there.
366s autopkgtest [21:24:14]: test autodep8-python3: -----------------------]
367s autodep8-python3     FAIL non-zero exit status 1
367s autopkgtest [21:24:15]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
367s autopkgtest [21:24:15]: @@@@@@@@@@@@@@@@@@@@ summary
367s run-unit-test        PASS
367s autodep8-python3     FAIL non-zero exit status 1
371s nova [W] Using flock in prodstack6-ppc64el
371s Creating nova instance adt-plucky-ppc64el-python-biom-format-20241113-211808-juju-7f2275-prod-proposed-migration-environment-15-76de6dfe-f1de-4c77-941c-7aaa02341df4 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...
371s nova [W] Using flock in prodstack6-ppc64el
371s Creating nova instance adt-plucky-ppc64el-python-biom-format-20241113-211808-juju-7f2275-prod-proposed-migration-environment-15-76de6dfe-f1de-4c77-941c-7aaa02341df4 from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...