0s autopkgtest [10:32:23]: starting date and time: 2024-11-13 10:32:23+0000
  0s autopkgtest [10:32:23]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [10:32:23]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hlp3pdrj/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 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@bos03-arm64-50.secgroup --name adt-plucky-arm64-python-biom-format-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-9a98a53d-90ad-4b4c-bb6d-5c253986a92a --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/
100s autopkgtest [10:34:03]: testbed dpkg architecture: arm64
101s autopkgtest [10:34:04]: testbed apt version: 2.9.8
101s autopkgtest [10:34:04]: @@@@@@@@@@@@@@@@@@@@ test bed setup
102s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
102s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
102s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
102s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
102s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
102s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
102s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
102s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
103s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
103s Fetched 1794 kB in 1s (2090 kB/s)
103s Reading package lists...
107s Reading package lists...
107s Building dependency tree...
107s Reading state information...
108s Calculating upgrade...
109s The following NEW packages will be installed:
109s   python3.13-gdbm
109s The following packages will be upgraded:
109s   libpython3-stdlib python3 python3-gdbm python3-minimal
109s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
109s Need to get 101 kB of archives.
109s After this operation, 141 kB of additional disk space will be used.
109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
110s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
110s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
110s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
110s Fetched 101 kB in 0s (281 kB/s)
111s (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 ... 79924 files and directories currently installed.)
111s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
111s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
111s Setting up python3-minimal (3.12.7-1) ...
111s (Reading database ... 
(Reading database ... 5%
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(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 ... 79924 files and directories currently installed.)
111s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
111s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ...
111s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
111s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
111s Selecting previously unselected package python3.13-gdbm.
111s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ...
111s Unpacking python3.13-gdbm (3.13.0-2) ...
111s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
111s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
111s Setting up python3.13-gdbm (3.13.0-2) ...
111s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
111s Setting up python3 (3.12.7-1) ...
112s Setting up python3-gdbm:arm64 (3.12.7-1) ...
112s Processing triggers for man-db (2.12.1-3) ...
113s Reading package lists...
114s Building dependency tree...
114s Reading state information...
115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
116s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
116s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
116s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
116s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
118s Reading package lists...
118s Reading package lists...
118s Building dependency tree...
118s Reading state information...
120s Calculating upgrade...
120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
120s Reading package lists...
120s Building dependency tree...
120s Reading state information...
122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
132s autopkgtest [10:34:35]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024
133s autopkgtest [10:34:36]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format
141s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B]
141s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB]
141s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB]
141s gpgv: Signature made Mon May 27 20:43:46 2024 UTC
141s gpgv:                using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
141s gpgv:                issuer "emollier@debian.org"
141s gpgv: Can't check signature: No public key
141s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found
142s autopkgtest [10:34:45]: testing package python-biom-format version 2.1.16-1
145s autopkgtest [10:34:48]: build not needed
156s autopkgtest [10:34:59]: test run-unit-test: preparing testbed
163s Reading package lists...
164s Building dependency tree...
164s Reading state information...
165s Starting pkgProblemResolver with broken count: 0
165s Starting 2 pkgProblemResolver with broken count: 0
165s Done
166s The following additional packages will be installed:
166s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64
166s   libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1
166s   libsz2 python-biom-format-doc python3-biom-format python3-click
166s   python3-colorama python3-dateutil python3-decorator python3-h5py
166s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
166s   python3-scipy python3-six python3-tz
166s Suggested packages:
166s   python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest
166s   python-pandas-doc python3-statsmodels python-scipy-doc
166s Recommended packages:
166s   javascript-common python3-matplotlib python3-bottleneck python3-numexpr
166s   python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml
166s   python3-tables g++ | c++-compiler python3-pil
166s The following NEW packages will be installed:
166s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
166s   libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
166s   liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format
166s   python3-click python3-colorama python3-dateutil python3-decorator
166s   python3-h5py python3-h5py-serial python3-numpy python3-pandas
166s   python3-pandas-lib python3-scipy python3-six python3-tz
166s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded.
166s Need to get 33.8 MB/33.8 MB of archives.
166s After this operation, 151 MB of additional disk space will be used.
166s Get:1 /tmp/autopkgtest.IpCbNL/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [724 B]
166s Get:2 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
167s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
167s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
167s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
167s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB]
167s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB]
167s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
167s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
167s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-sphinxdoc all 7.4.7-4 [158 kB]
167s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
167s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
167s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
167s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python-biom-format-doc all 2.1.16-1 [57.5 kB]
167s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
167s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB]
167s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
167s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB]
167s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB]
167s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB]
167s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB]
167s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB]
167s Get:23 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB]
167s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
167s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
167s Get:26 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB]
168s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1 [137 kB]
168s Fetched 33.8 MB in 2s (22.3 MB/s)
168s Selecting previously unselected package libaec0:arm64.
168s (Reading database ... 
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(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 ... 79931 files and directories currently installed.)
168s Preparing to unpack .../00-libaec0_1.1.3-1_arm64.deb ...
168s Unpacking libaec0:arm64 (1.1.3-1) ...
168s Selecting previously unselected package libblas3:arm64.
168s Preparing to unpack .../01-libblas3_3.12.0-3build2_arm64.deb ...
168s Unpacking libblas3:arm64 (3.12.0-3build2) ...
169s Selecting previously unselected package libgfortran5:arm64.
169s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_arm64.deb ...
169s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ...
169s Selecting previously unselected package libsz2:arm64.
169s Preparing to unpack .../03-libsz2_1.1.3-1_arm64.deb ...
169s Unpacking libsz2:arm64 (1.1.3-1) ...
169s Selecting previously unselected package libhdf5-103-1t64:arm64.
169s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_arm64.deb ...
169s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ...
169s Selecting previously unselected package libhdf5-hl-100t64:arm64.
169s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_arm64.deb ...
169s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ...
169s Selecting previously unselected package libjs-jquery.
169s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
169s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
169s Selecting previously unselected package libjs-underscore.
169s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
169s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
169s Selecting previously unselected package libjs-sphinxdoc.
169s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ...
169s Unpacking libjs-sphinxdoc (7.4.7-4) ...
169s Selecting previously unselected package liblapack3:arm64.
169s Preparing to unpack .../09-liblapack3_3.12.0-3build2_arm64.deb ...
169s Unpacking liblapack3:arm64 (3.12.0-3build2) ...
169s Selecting previously unselected package liblbfgsb0:arm64.
169s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ...
169s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
169s Selecting previously unselected package liblzf1:arm64.
169s Preparing to unpack .../11-liblzf1_3.6-4_arm64.deb ...
169s Unpacking liblzf1:arm64 (3.6-4) ...
169s Selecting previously unselected package python-biom-format-doc.
169s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ...
169s Unpacking python-biom-format-doc (2.1.16-1) ...
169s Selecting previously unselected package python3-numpy.
169s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ...
169s Unpacking python3-numpy (1:1.26.4+ds-11build1) ...
169s Selecting previously unselected package python3-h5py-serial.
169s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_arm64.deb ...
169s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
169s Selecting previously unselected package python3-h5py.
169s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ...
169s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
169s Selecting previously unselected package python3-colorama.
169s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ...
169s Unpacking python3-colorama (0.4.6-4) ...
170s Selecting previously unselected package python3-click.
170s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ...
170s Unpacking python3-click (8.1.7-2) ...
170s Selecting previously unselected package python3-six.
170s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ...
170s Unpacking python3-six (1.16.0-7) ...
170s Selecting previously unselected package python3-dateutil.
170s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ...
170s Unpacking python3-dateutil (2.9.0-2) ...
170s Selecting previously unselected package python3-tz.
170s Preparing to unpack .../20-python3-tz_2024.1-2_all.deb ...
170s Unpacking python3-tz (2024.1-2) ...
170s Selecting previously unselected package python3-pandas-lib:arm64.
170s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-5_arm64.deb ...
170s Unpacking python3-pandas-lib:arm64 (2.2.3+dfsg-5) ...
170s Selecting previously unselected package python3-pandas.
170s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-5_all.deb ...
170s Unpacking python3-pandas (2.2.3+dfsg-5) ...
170s Selecting previously unselected package python3-decorator.
170s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ...
170s Unpacking python3-decorator (5.1.1-5) ...
170s Selecting previously unselected package python3-scipy.
170s Preparing to unpack .../24-python3-scipy_1.13.1-5_arm64.deb ...
170s Unpacking python3-scipy (1.13.1-5) ...
171s Selecting previously unselected package python3-biom-format.
171s Preparing to unpack .../25-python3-biom-format_2.1.16-1_arm64.deb ...
171s Unpacking python3-biom-format (2.1.16-1) ...
171s Selecting previously unselected package autopkgtest-satdep.
171s Preparing to unpack .../26-1-autopkgtest-satdep.deb ...
171s Unpacking autopkgtest-satdep (0) ...
171s Setting up python3-colorama (0.4.6-4) ...
171s Setting up python3-click (8.1.7-2) ...
171s Setting up libaec0:arm64 (1.1.3-1) ...
171s Setting up python3-tz (2024.1-2) ...
171s Setting up python3-six (1.16.0-7) ...
172s Setting up python3-decorator (5.1.1-5) ...
172s Setting up libblas3:arm64 (3.12.0-3build2) ...
172s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
172s Setting up liblzf1:arm64 (3.6-4) ...
172s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
172s Setting up python3-dateutil (2.9.0-2) ...
172s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
172s Setting up libsz2:arm64 (1.1.3-1) ...
172s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
172s Setting up liblapack3:arm64 (3.12.0-3build2) ...
172s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
172s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
174s Setting up libjs-sphinxdoc (7.4.7-4) ...
174s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ...
174s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
174s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ...
174s Setting up python3-scipy (1.13.1-5) ...
179s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ...
179s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
179s Setting up python-biom-format-doc (2.1.16-1) ...
179s Setting up python3-pandas (2.2.3+dfsg-5) ...
185s Setting up python3-h5py (3.11.0-5ubuntu1) ...
185s Setting up python3-biom-format (2.1.16-1) ...
186s Setting up autopkgtest-satdep (0) ...
186s Processing triggers for man-db (2.12.1-3) ...
186s Processing triggers for libc-bin (2.40-1ubuntu3) ...
195s (Reading database ... 84444 files and directories currently installed.)
195s Removing autopkgtest-satdep (0) ...
198s autopkgtest [10:35:41]: test run-unit-test: [-----------------------
201s 
201s System information
201s ==================
201s          Platform:	linux
201s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
201s Python executable:	/usr/bin/python3
201s 
201s Dependency versions
201s ===================
201s click version:	8.1.7
201s NumPy version:	1.26.4
201s SciPy version:	1.13.1
201s  h5py version:	3.11.0
201s 
201s biom-format package information
201s ===============================
201s biom-format version:	2.1.16
201s 
202s 
202s The input file is a valid BIOM-formatted file.
204s 
204s The input file is a valid BIOM-formatted file.
205s 
205s The input file is a valid BIOM-formatted file.
207s 
207s The input file is a valid BIOM-formatted file.
210s + table=examples/min_sparse_otu_table_hdf5.biom
210s + obsmd=examples/obs_md.txt
210s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ]
210s + biom show-install-info
211s 
211s System information
211s ==================
211s          Platform:	linux
211s    Python version:	3.12.7 (main, Nov  8 2024, 17:55:36) [GCC 14.2.0]
211s Python executable:	/usr/bin/python3
211s 
211s Dependency versions
211s ===================
211s click version:	8.1.7
211s NumPy version:	1.26.4
211s SciPy version:	1.13.1
211s  h5py version:	3.11.0
211s 
211s biom-format package information
211s ===============================
211s biom-format version:	2.1.16
211s 
212s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom
213s 
213s The input file is a valid BIOM-formatted file.
213s + 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
215s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json
217s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv
219s + biom validate-table -i test_json.biom
220s 
220s The input file is a valid BIOM-formatted file.
220s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5
222s + biom validate-table -i test_hdf5.biom
223s 
223s The input file is a valid BIOM-formatted file.
223s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv
224s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table
226s + biom validate-table -i test_hdf5.biom
227s 
227s The input file is a valid BIOM-formatted file.
227s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table
228s + biom validate-table -i test_json.biom
230s 
230s The input file is a valid BIOM-formatted file.
230s + biom head -i examples/min_sparse_otu_table_hdf5.biom
231s # Constructed from biom file
231s #OTU ID	Sample1	Sample2	Sample3	Sample4	Sample5
231s GG_OTU_1	0.0	0.0	1.0	0.0	0.0
231s GG_OTU_2	5.0	1.0	0.0	2.0	3.0
231s GG_OTU_3	0.0	0.0	1.0	4.0	0.0
231s GG_OTU_4	2.0	1.0	1.0	0.0	0.0
231s GG_OTU_5	0.0	1.0	1.0	0.0	0.0
232s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom
233s Sample1
233s Sample2
233s Sample3
233s Sample4
233s Sample5
233s Sample6
234s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p
235s + cat
235s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt
236s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom
237s Num samples: 6
237s Num observations: 5
237s Total count: 27
237s Table density (fraction of non-zero values): 0.500
237s 
237s Counts/sample summary:
237s  Min: 3.000
237s  Max: 7.000
237s  Median: 4.000
237s  Mean: 4.500
237s  Std. dev.: 1.500
237s  Sample Metadata Categories: None provided
237s  Observation Metadata Categories: None provided
237s 
237s Counts/sample detail:
237s Sample2: 3.000
237s Sample5: 3.000
237s Sample3: 4.000
237s Sample6: 4.000
237s Sample4: 6.000
237s Sample1: 7.000
237s + cat
237s + biom from-uc -i uctest -o test_uc.biom
239s If this message was shown, then all commands executed without failure
239s + echo If this message was shown, then all commands executed without failure
239s autopkgtest [10:36:22]: test run-unit-test: -----------------------]
240s autopkgtest [10:36:23]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
240s run-unit-test        PASS
240s autopkgtest [10:36:23]: test autodep8-python3: preparing testbed
370s autopkgtest [10:38:33]: testbed dpkg architecture: arm64
370s autopkgtest [10:38:33]: testbed apt version: 2.9.8
370s autopkgtest [10:38:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup
371s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
371s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
371s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB]
372s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB]
372s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
372s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB]
372s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB]
372s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB]
372s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB]
372s Fetched 1794 kB in 1s (1301 kB/s)
372s Reading package lists...
375s Reading package lists...
375s Building dependency tree...
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376s Calculating upgrade...
377s The following NEW packages will be installed:
377s   python3.13-gdbm
377s The following packages will be upgraded:
377s   libpython3-stdlib python3 python3-gdbm python3-minimal
377s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
377s Need to get 101 kB of archives.
377s After this operation, 141 kB of additional disk space will be used.
377s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB]
377s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB]
377s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB]
377s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB]
377s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B]
378s Fetched 101 kB in 0s (284 kB/s)
378s (Reading database ... 
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378s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ...
378s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ...
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378s Preparing to unpack .../python3_3.12.7-1_arm64.deb ...
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379s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ...
379s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ...
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379s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ...
379s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ...
379s Setting up python3.13-gdbm (3.13.0-2) ...
379s Setting up libpython3-stdlib:arm64 (3.12.7-1) ...
379s Setting up python3 (3.12.7-1) ...
379s Setting up python3-gdbm:arm64 (3.12.7-1) ...
379s Processing triggers for man-db (2.12.1-3) ...
380s Reading package lists...
381s Building dependency tree...
381s Reading state information...
381s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
382s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
382s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
382s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
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383s Reading package lists...
383s Reading package lists...
384s Building dependency tree...
384s Reading state information...
384s Calculating upgrade...
385s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
385s Reading package lists...
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385s Reading state information...
386s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
393s Reading package lists...
394s Building dependency tree...
394s Reading state information...
394s Starting pkgProblemResolver with broken count: 0
394s Starting 2 pkgProblemResolver with broken count: 0
394s Done
395s The following additional packages will be installed:
395s   libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3
395s   liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2
395s   python3-all python3-biom-format python3-click python3-colorama
395s   python3-dateutil python3-decorator python3-h5py python3-h5py-serial
395s   python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-six
395s   python3-tz python3.13 python3.13-minimal
395s Suggested packages:
395s   python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc
395s   python3-dev python3-pytest python-pandas-doc python3-statsmodels
395s   python-scipy-doc python3.13-venv python3.13-doc binfmt-support
395s Recommended packages:
395s   python3-matplotlib python3-bottleneck python3-numexpr python3-odf
395s   python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables
395s   g++ | c++-compiler python3-pil
395s The following NEW packages will be installed:
395s   autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64
395s   libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal
395s   libpython3.13-stdlib libsz2 python3-all python3-biom-format python3-click
395s   python3-colorama python3-dateutil python3-decorator python3-h5py
395s   python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib
395s   python3-scipy python3-six python3-tz python3.13 python3.13-minimal
395s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded.
395s Need to get 38.9 MB/38.9 MB of archives.
395s After this operation, 174 MB of additional disk space will be used.
395s Get:1 /tmp/autopkgtest.IpCbNL/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B]
395s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB]
396s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB]
397s Get:4 http://ftpmaster.internal/ubuntu plucky/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB]
397s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB]
397s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB]
397s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 libsz2 arm64 1.1.3-1 [5254 B]
397s Get:8 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-4ubuntu3 [1207 kB]
397s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-4ubuntu3 [56.9 kB]
398s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB]
398s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB]
398s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblzf1 arm64 3.6-4 [7426 B]
398s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB]
398s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB]
398s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B]
398s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB]
398s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py-serial arm64 3.11.0-5ubuntu1 [1064 kB]
398s Get:18 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-h5py all 3.11.0-5ubuntu1 [7974 B]
398s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-colorama all 0.4.6-4 [32.1 kB]
398s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-click all 8.1.7-2 [79.5 kB]
398s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-six all 1.16.0-7 [13.1 kB]
398s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB]
399s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-tz all 2024.1-2 [31.4 kB]
399s Get:24 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas-lib arm64 2.2.3+dfsg-5 [4422 kB]
399s Get:25 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pandas all 2.2.3+dfsg-5 [3112 kB]
399s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB]
399s Get:27 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB]
400s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-biom-format arm64 2.1.16-1 [137 kB]
400s Fetched 38.9 MB in 4s (8704 kB/s)
400s Selecting previously unselected package libpython3.13-minimal:arm64.
400s (Reading database ... 
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400s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ...
400s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ...
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400s Unpacking libaec0:arm64 (1.1.3-1) ...
400s Selecting previously unselected package libblas3:arm64.
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404s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ...
404s Setting up python3-decorator (5.1.1-5) ...
404s Setting up libblas3:arm64 (3.12.0-3build2) ...
404s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode
404s Setting up liblzf1:arm64 (3.6-4) ...
404s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ...
404s Setting up python3.13-minimal (3.13.0-2) ...
405s Setting up python3-dateutil (2.9.0-2) ...
406s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ...
406s Setting up libsz2:arm64 (1.1.3-1) ...
406s Setting up liblapack3:arm64 (3.12.0-3build2) ...
406s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode
406s Setting up python3.13 (3.13.0-2) ...
407s Setting up python3-all (3.12.7-1) ...
407s Setting up python3-numpy (1:1.26.4+ds-11build1) ...
411s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-4ubuntu3) ...
411s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ...
411s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-4ubuntu3) ...
411s Setting up python3-scipy (1.13.1-5) ...
419s Setting up python3-pandas-lib:arm64 (2.2.3+dfsg-5) ...
419s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
420s Setting up python3-pandas (2.2.3+dfsg-5) ...
431s Setting up python3-h5py (3.11.0-5ubuntu1) ...
431s Setting up python3-biom-format (2.1.16-1) ...
432s Setting up autopkgtest-satdep (0) ...
432s Processing triggers for systemd (256.5-2ubuntu4) ...
432s Processing triggers for man-db (2.12.1-3) ...
432s Processing triggers for libc-bin (2.40-1ubuntu3) ...
436s (Reading database ... 85080 files and directories currently installed.)
436s Removing autopkgtest-satdep (0) ...
440s autopkgtest [10:39:43]: 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
440s autopkgtest [10:39:43]: test autodep8-python3: [-----------------------
441s Testing with python3.13:
441s Traceback (most recent call last):
441s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in <module>
441s     from . import multiarray
441s   File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in <module>
441s     from . import overrides
441s   File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in <module>
441s     from numpy.core._multiarray_umath import (
441s         add_docstring,  _get_implementing_args, _ArrayFunctionDispatcher)
441s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath'
441s 
441s During handling of the above exception, another exception occurred:
441s 
441s Traceback (most recent call last):
441s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in <module>
441s     from numpy.__config__ import show as show_config
441s   File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
441s     from numpy.core._multiarray_umath import (
441s     ...<3 lines>...
441s     )
441s   File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in <module>
441s     raise ImportError(msg)
441s ImportError: 
441s 
441s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
441s 
441s Importing the numpy C-extensions failed. This error can happen for
441s many reasons, often due to issues with your setup or how NumPy was
441s installed.
441s 
441s We have compiled some common reasons and troubleshooting tips at:
441s 
441s     https://numpy.org/devdocs/user/troubleshooting-importerror.html
441s 
441s Please note and check the following:
441s 
441s   * The Python version is: Python3.13 from "/usr/bin/python3.13"
441s   * The NumPy version is: "1.26.4"
441s 
441s and make sure that they are the versions you expect.
441s Please carefully study the documentation linked above for further help.
441s 
441s Original error was: No module named 'numpy.core._multiarray_umath'
441s 
441s 
441s The above exception was the direct cause of the following exception:
441s 
441s Traceback (most recent call last):
441s   File "<string>", line 1, in <module>
441s     import biom; print(biom)
441s     ^^^^^^^^^^^
441s   File "/usr/lib/python3/dist-packages/biom/__init__.py", line 51, in <module>
441s     from .table import Table
441s   File "/usr/lib/python3/dist-packages/biom/table.py", line 174, in <module>
441s     import numpy as np
441s   File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in <module>
441s     raise ImportError(msg) from e
441s ImportError: Error importing numpy: you should not try to import numpy from
441s         its source directory; please exit the numpy source tree, and relaunch
441s         your python interpreter from there.
441s autopkgtest [10:39:44]: test autodep8-python3: -----------------------]
442s autopkgtest [10:39:45]: test autodep8-python3:  - - - - - - - - - - results - - - - - - - - - -
442s autodep8-python3     FAIL non-zero exit status 1
442s autopkgtest [10:39:45]: @@@@@@@@@@@@@@@@@@@@ summary
442s run-unit-test        PASS
442s autodep8-python3     FAIL non-zero exit status 1
455s nova [W] Skipping flock in bos03-arm64
455s Creating nova instance adt-plucky-arm64-python-biom-format-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-9a98a53d-90ad-4b4c-bb6d-5c253986a92a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...
455s nova [W] Skipping flock in bos03-arm64
455s Creating nova instance adt-plucky-arm64-python-biom-format-20241113-101405-juju-7f2275-prod-proposed-migration-environment-20-9a98a53d-90ad-4b4c-bb6d-5c253986a92a from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...