0s autopkgtest [21:23:26]: starting date and time: 2024-11-13 21:23:26+0000 0s autopkgtest [21:23:26]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [21:23:26]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.a0dm81l2/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --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' -- lxd -r lxd-armhf-10.145.243.240 lxd-armhf-10.145.243.240:autopkgtest/ubuntu/plucky/armhf 52s autopkgtest [21:24:18]: testbed dpkg architecture: armhf 54s autopkgtest [21:24:20]: testbed apt version: 2.9.8 54s autopkgtest [21:24:20]: @@@@@@@@@@@@@@@@@@@@ test bed setup 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 63s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 63s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 63s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 64s Fetched 1951 kB in 1s (1811 kB/s) 64s Reading package lists... 81s tee: /proc/self/fd/2: Permission denied 104s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 105s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 105s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 105s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 106s Reading package lists... 106s Reading package lists... 106s Building dependency tree... 106s Reading state information... 107s Calculating upgrade... 107s The following NEW packages will be installed: 107s python3.13-gdbm 107s The following packages will be upgraded: 107s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 107s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 107s python3-newt whiptail 108s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 108s Need to get 1207 kB of archives. 108s After this operation, 124 kB of additional disk space will be used. 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 108s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 108s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 108s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 108s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 108s Fetched 1207 kB in 1s (1960 kB/s) 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 109s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Setting up python3-minimal (3.12.7-1) ... 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 109s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 109s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 109s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 109s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 109s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 109s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 109s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 109s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 109s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 109s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 109s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 109s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 109s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 109s Selecting previously unselected package python3.13-gdbm. 109s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 109s Unpacking python3.13-gdbm (3.13.0-2) ... 109s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 109s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 109s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 109s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 109s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 109s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 109s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 109s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 110s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 110s Setting up libutempter0:armhf (1.2.1-4) ... 110s Setting up whiptail (0.52.24-2ubuntu4) ... 110s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 110s Setting up python3.13-gdbm (3.13.0-2) ... 110s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 110s Setting up python3 (3.12.7-1) ... 110s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 110s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 110s Setting up python3-gdbm:armhf (3.12.7-1) ... 110s Processing triggers for man-db (2.12.1-3) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 112s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s autopkgtest [21:25:20]: rebooting testbed after setup commands that affected boot 183s autopkgtest [21:26:29]: testbed running kernel: Linux 6.8.0-48-generic #48~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Oct 7 11:49:53 UTC 2 212s autopkgtest [21:26:58]: @@@@@@@@@@@@@@@@@@@@ apt-source python-biom-format 227s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (dsc) [2628 B] 227s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (tar) [11.9 MB] 227s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-biom-format 2.1.16-1 (diff) [11.6 kB] 227s gpgv: Signature made Mon May 27 20:43:46 2024 UTC 227s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 227s gpgv: issuer "emollier@debian.org" 227s gpgv: Can't check signature: No public key 227s dpkg-source: warning: cannot verify inline signature for ./python-biom-format_2.1.16-1.dsc: no acceptable signature found 228s autopkgtest [21:27:14]: testing package python-biom-format version 2.1.16-1 230s autopkgtest [21:27:16]: build not needed 234s autopkgtest [21:27:20]: test run-unit-test: preparing testbed 244s Reading package lists... 244s Building dependency tree... 244s Reading state information... 245s Starting pkgProblemResolver with broken count: 0 245s Starting 2 pkgProblemResolver with broken count: 0 245s Done 246s The following additional packages will be installed: 246s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 246s libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblzf1 246s libsz2 python-biom-format-doc python3-biom-format python3-click 246s python3-colorama python3-dateutil python3-decorator python3-h5py 246s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 246s python3-scipy python3-six python3-tz 246s Suggested packages: 246s python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest 246s python-pandas-doc python3-statsmodels python-scipy-doc 246s Recommended packages: 246s javascript-common python3-matplotlib python3-bottleneck python3-numexpr 246s python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml 246s python3-tables g++ | c++-compiler python3-pil 246s The following NEW packages will be installed: 246s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 246s libhdf5-hl-100t64 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 246s liblbfgsb0 liblzf1 libsz2 python-biom-format-doc python3-biom-format 246s python3-click python3-colorama python3-dateutil python3-decorator 246s python3-h5py python3-h5py-serial python3-numpy python3-pandas 246s python3-pandas-lib python3-scipy python3-six python3-tz 246s 0 upgraded, 27 newly installed, 0 to remove and 0 not upgraded. 246s Need to get 33.9 MB/33.9 MB of archives. 246s After this operation, 126 MB of additional disk space will be used. 246s Get:1 /tmp/autopkgtest.oPIwKo/1-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 246s Get:2 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 246s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 246s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 246s Get:5 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 246s Get:6 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 246s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 246s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 246s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB] 246s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjs-sphinxdoc all 7.4.7-4 [158 kB] 246s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 247s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 247s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 247s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf python-biom-format-doc all 2.1.16-1 [57.5 kB] 247s Get:15 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 247s Get:16 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 247s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 247s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 247s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 247s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 247s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 247s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 247s Get:23 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB] 247s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB] 247s Get:25 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 247s Get:26 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 247s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1 [135 kB] 248s Fetched 33.9 MB in 2s (19.2 MB/s) 248s Selecting previously unselected package libaec0:armhf. 248s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59567 files and directories currently installed.) 248s Preparing to unpack .../00-libaec0_1.1.3-1_armhf.deb ... 248s Unpacking libaec0:armhf (1.1.3-1) ... 248s Selecting previously unselected package libblas3:armhf. 248s Preparing to unpack .../01-libblas3_3.12.0-3build2_armhf.deb ... 248s Unpacking libblas3:armhf (3.12.0-3build2) ... 248s Selecting previously unselected package libgfortran5:armhf. 248s Preparing to unpack .../02-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 248s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 248s Selecting previously unselected package libsz2:armhf. 248s Preparing to unpack .../03-libsz2_1.1.3-1_armhf.deb ... 248s Unpacking libsz2:armhf (1.1.3-1) ... 248s Selecting previously unselected package libhdf5-103-1t64:armhf. 248s Preparing to unpack .../04-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 248s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 248s Selecting previously unselected package libhdf5-hl-100t64:armhf. 248s Preparing to unpack .../05-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 248s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 248s Selecting previously unselected package libjs-jquery. 248s Preparing to unpack .../06-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 248s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 248s Selecting previously unselected package libjs-underscore. 248s Preparing to unpack .../07-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... 248s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 248s Selecting previously unselected package libjs-sphinxdoc. 248s Preparing to unpack .../08-libjs-sphinxdoc_7.4.7-4_all.deb ... 248s Unpacking libjs-sphinxdoc (7.4.7-4) ... 248s Selecting previously unselected package liblapack3:armhf. 248s Preparing to unpack .../09-liblapack3_3.12.0-3build2_armhf.deb ... 248s Unpacking liblapack3:armhf (3.12.0-3build2) ... 248s Selecting previously unselected package liblbfgsb0:armhf. 248s Preparing to unpack .../10-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 248s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 248s Selecting previously unselected package liblzf1:armhf. 248s Preparing to unpack .../11-liblzf1_3.6-4_armhf.deb ... 248s Unpacking liblzf1:armhf (3.6-4) ... 248s Selecting previously unselected package python-biom-format-doc. 248s Preparing to unpack .../12-python-biom-format-doc_2.1.16-1_all.deb ... 248s Unpacking python-biom-format-doc (2.1.16-1) ... 248s Selecting previously unselected package python3-numpy. 248s Preparing to unpack .../13-python3-numpy_1%3a1.26.4+ds-11build1_armhf.deb ... 248s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 249s Selecting previously unselected package python3-h5py-serial. 249s Preparing to unpack .../14-python3-h5py-serial_3.11.0-5ubuntu1_armhf.deb ... 249s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ... 249s Selecting previously unselected package python3-h5py. 249s Preparing to unpack .../15-python3-h5py_3.11.0-5ubuntu1_all.deb ... 249s Unpacking python3-h5py (3.11.0-5ubuntu1) ... 249s Selecting previously unselected package python3-colorama. 249s Preparing to unpack .../16-python3-colorama_0.4.6-4_all.deb ... 249s Unpacking python3-colorama (0.4.6-4) ... 249s Selecting previously unselected package python3-click. 249s Preparing to unpack .../17-python3-click_8.1.7-2_all.deb ... 249s Unpacking python3-click (8.1.7-2) ... 249s Selecting previously unselected package python3-six. 249s Preparing to unpack .../18-python3-six_1.16.0-7_all.deb ... 249s Unpacking python3-six (1.16.0-7) ... 249s Selecting previously unselected package python3-dateutil. 249s Preparing to unpack .../19-python3-dateutil_2.9.0-2_all.deb ... 249s Unpacking python3-dateutil (2.9.0-2) ... 249s Selecting previously unselected package python3-tz. 249s Preparing to unpack .../20-python3-tz_2024.1-2_all.deb ... 249s Unpacking python3-tz (2024.1-2) ... 249s Selecting previously unselected package python3-pandas-lib:armhf. 249s Preparing to unpack .../21-python3-pandas-lib_2.2.3+dfsg-5_armhf.deb ... 249s Unpacking python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 249s Selecting previously unselected package python3-pandas. 249s Preparing to unpack .../22-python3-pandas_2.2.3+dfsg-5_all.deb ... 249s Unpacking python3-pandas (2.2.3+dfsg-5) ... 250s Selecting previously unselected package python3-decorator. 250s Preparing to unpack .../23-python3-decorator_5.1.1-5_all.deb ... 250s Unpacking python3-decorator (5.1.1-5) ... 250s Selecting previously unselected package python3-scipy. 250s Preparing to unpack .../24-python3-scipy_1.13.1-5_armhf.deb ... 250s Unpacking python3-scipy (1.13.1-5) ... 250s Selecting previously unselected package python3-biom-format. 250s Preparing to unpack .../25-python3-biom-format_2.1.16-1_armhf.deb ... 250s Unpacking python3-biom-format (2.1.16-1) ... 250s Selecting previously unselected package autopkgtest-satdep. 250s Preparing to unpack .../26-1-autopkgtest-satdep.deb ... 250s Unpacking autopkgtest-satdep (0) ... 250s Setting up python3-colorama (0.4.6-4) ... 251s Setting up python3-click (8.1.7-2) ... 251s Setting up libaec0:armhf (1.1.3-1) ... 251s Setting up python3-tz (2024.1-2) ... 251s Setting up python3-six (1.16.0-7) ... 251s Setting up python3-decorator (5.1.1-5) ... 251s Setting up libblas3:armhf (3.12.0-3build2) ... 251s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 251s Setting up liblzf1:armhf (3.6-4) ... 251s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 251s Setting up python3-dateutil (2.9.0-2) ... 251s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 251s Setting up libsz2:armhf (1.1.3-1) ... 251s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 251s Setting up liblapack3:armhf (3.12.0-3build2) ... 251s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 251s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 253s Setting up libjs-sphinxdoc (7.4.7-4) ... 253s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 253s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 253s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 253s Setting up python3-scipy (1.13.1-5) ... 257s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 257s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 258s Setting up python-biom-format-doc (2.1.16-1) ... 258s Setting up python3-pandas (2.2.3+dfsg-5) ... 263s Setting up python3-h5py (3.11.0-5ubuntu1) ... 264s Setting up python3-biom-format (2.1.16-1) ... 264s Setting up autopkgtest-satdep (0) ... 264s Processing triggers for man-db (2.12.1-3) ... 265s Processing triggers for libc-bin (2.40-1ubuntu3) ... 280s (Reading database ... 64081 files and directories currently installed.) 280s Removing autopkgtest-satdep (0) ... 286s autopkgtest [21:28:12]: test run-unit-test: [----------------------- 289s 289s System information 289s ================== 289s Platform: linux 289s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 289s Python executable: /usr/bin/python3 289s 289s Dependency versions 289s =================== 289s click version: 8.1.7 289s NumPy version: 1.26.4 289s SciPy version: 1.13.1 289s h5py version: 3.11.0 289s 289s biom-format package information 289s =============================== 289s biom-format version: 2.1.16 289s 290s 290s The input file is a valid BIOM-formatted file. 291s 291s The input file is a valid BIOM-formatted file. 292s 292s The input file is a valid BIOM-formatted file. 293s 293s The input file is a valid BIOM-formatted file. 295s + table=examples/min_sparse_otu_table_hdf5.biom 295s + obsmd=examples/obs_md.txt 295s + [ ! -f examples/min_sparse_otu_table_hdf5.biom ] 295s + biom show-install-info 296s 296s System information 296s ================== 296s Platform: linux 296s Python version: 3.12.7 (main, Nov 8 2024, 17:55:36) [GCC 14.2.0] 296s Python executable: /usr/bin/python3 296s 296s Dependency versions 296s =================== 296s click version: 8.1.7 296s NumPy version: 1.26.4 296s SciPy version: 1.13.1 296s h5py version: 3.11.0 296s 296s biom-format package information 296s =============================== 296s biom-format version: 2.1.16 296s 296s + biom validate-table -i examples/min_sparse_otu_table_hdf5.biom 297s 297s The input file is a valid BIOM-formatted file. 297s + 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 298s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_json.biom --to-json 299s + biom convert -i examples/min_sparse_otu_table_hdf5.biom -o test_tsv.txt --to-tsv 300s + biom validate-table -i test_json.biom 301s 301s The input file is a valid BIOM-formatted file. 301s + biom convert -i test_json.biom -o test_hdf5.biom --to-hdf5 302s + biom validate-table -i test_hdf5.biom 303s 303s The input file is a valid BIOM-formatted file. 303s + biom convert -i test_json.biom -o test_tsv.txt --to-tsv 304s + biom convert -i test_tsv.txt -o test_hdf5.biom --to-hdf5 --table-type OTU table 305s + biom validate-table -i test_hdf5.biom 306s 306s The input file is a valid BIOM-formatted file. 306s + biom convert -i test_tsv.txt -o test_json.biom --to-json --table-type OTU table 307s + biom validate-table -i test_json.biom 308s 308s The input file is a valid BIOM-formatted file. 308s + biom head -i examples/min_sparse_otu_table_hdf5.biom 309s # Constructed from biom file 309s #OTU ID Sample1 Sample2 Sample3 Sample4 Sample5 309s GG_OTU_1 0.0 0.0 1.0 0.0 0.0 309s GG_OTU_2 5.0 1.0 0.0 2.0 3.0 309s GG_OTU_3 0.0 0.0 1.0 4.0 0.0 309s GG_OTU_4 2.0 1.0 1.0 0.0 0.0 309s GG_OTU_5 0.0 1.0 1.0 0.0 0.0 309s + biom table-ids -i examples/min_sparse_otu_table_hdf5.biom 310s Sample1 310s Sample2 310s Sample3 310s Sample4 310s Sample5 310s Sample6 310s + biom normalize-table -i examples/min_sparse_otu_table_hdf5.biom -o test_norm.biom -p 311s + cat 311s + biom subset-table -i examples/min_sparse_otu_table_hdf5.biom -o test_subset.biom -a observation -s ids.txt 312s + biom summarize-table -i examples/min_sparse_otu_table_hdf5.biom 313s Num samples: 6 313s Num observations: 5 313s Total count: 27 313s Table density (fraction of non-zero values): 0.500 313s 313s Counts/sample summary: 313s Min: 3.000 313s Max: 7.000 313s Median: 4.000 313s Mean: 4.500 313s Std. dev.: 1.500 313s Sample Metadata Categories: None provided 313s Observation Metadata Categories: None provided 313s 313s Counts/sample detail: 313s Sample2: 3.000 313s Sample5: 3.000 313s Sample3: 4.000 313s Sample6: 4.000 313s Sample4: 6.000 313s Sample1: 7.000 313s + cat 313s + biom from-uc -i uctest -o test_uc.biom 314s + echo If this message was shown, then all commands executed without failure 314s If this message was shown, then all commands executed without failure 315s autopkgtest [21:28:41]: test run-unit-test: -----------------------] 319s run-unit-test PASS 319s autopkgtest [21:28:45]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 323s autopkgtest [21:28:49]: test autodep8-python3: preparing testbed 376s autopkgtest [21:29:42]: testbed dpkg architecture: armhf 378s autopkgtest [21:29:44]: testbed apt version: 2.9.8 378s autopkgtest [21:29:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup 386s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 386s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [101 kB] 386s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [970 kB] 387s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 387s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.2 kB] 387s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [104 kB] 387s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [662 kB] 387s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [17.2 kB] 387s Fetched 1951 kB in 1s (2136 kB/s) 387s Reading package lists... 403s tee: /proc/self/fd/2: Permission denied 424s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 424s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 424s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 424s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 426s Reading package lists... 426s Reading package lists... 426s Building dependency tree... 426s Reading state information... 427s Calculating upgrade... 427s The following NEW packages will be installed: 427s python3.13-gdbm 427s The following packages will be upgraded: 427s libgnutls30t64 libjson-glib-1.0-0 libjson-glib-1.0-common libnewt0.52 427s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 427s python3-newt whiptail 427s 11 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 427s Need to get 1207 kB of archives. 427s After this operation, 124 kB of additional disk space will be used. 427s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-minimal armhf 3.12.7-1 [27.4 kB] 427s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3 armhf 3.12.7-1 [24.0 kB] 427s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf libpython3-stdlib armhf 3.12.7-1 [10.0 kB] 427s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf libgnutls30t64 armhf 3.8.8-2ubuntu1 [955 kB] 428s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-newt armhf 0.52.24-2ubuntu4 [19.7 kB] 428s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libnewt0.52 armhf 0.52.24-2ubuntu4 [39.2 kB] 428s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf whiptail armhf 0.52.24-2ubuntu4 [17.2 kB] 428s Get:8 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-gdbm armhf 3.13.0-2 [29.5 kB] 428s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-gdbm armhf 3.12.7-1 [8642 B] 428s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 428s Get:11 http://ftpmaster.internal/ubuntu plucky/main armhf libjson-glib-1.0-0 armhf 1.10.0+ds-3 [61.7 kB] 428s Get:12 http://ftpmaster.internal/ubuntu plucky/main armhf libutempter0 armhf 1.2.1-4 [9062 B] 428s Fetched 1207 kB in 1s (1956 kB/s) 428s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 428s Preparing to unpack .../python3-minimal_3.12.7-1_armhf.deb ... 428s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 428s Setting up python3-minimal (3.12.7-1) ... 428s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 428s Preparing to unpack .../python3_3.12.7-1_armhf.deb ... 429s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 429s Preparing to unpack .../libpython3-stdlib_3.12.7-1_armhf.deb ... 429s Unpacking libpython3-stdlib:armhf (3.12.7-1) over (3.12.6-0ubuntu1) ... 429s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_armhf.deb ... 429s Unpacking libgnutls30t64:armhf (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 429s Setting up libgnutls30t64:armhf (3.8.8-2ubuntu1) ... 429s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59559 files and directories currently installed.) 429s Preparing to unpack .../0-python3-newt_0.52.24-2ubuntu4_armhf.deb ... 429s Unpacking python3-newt:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 429s Preparing to unpack .../1-libnewt0.52_0.52.24-2ubuntu4_armhf.deb ... 429s Unpacking libnewt0.52:armhf (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 429s Preparing to unpack .../2-whiptail_0.52.24-2ubuntu4_armhf.deb ... 429s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ... 429s Selecting previously unselected package python3.13-gdbm. 429s Preparing to unpack .../3-python3.13-gdbm_3.13.0-2_armhf.deb ... 429s Unpacking python3.13-gdbm (3.13.0-2) ... 429s Preparing to unpack .../4-python3-gdbm_3.12.7-1_armhf.deb ... 429s Unpacking python3-gdbm:armhf (3.12.7-1) over (3.12.6-1ubuntu1) ... 429s Preparing to unpack .../5-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 429s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 429s Preparing to unpack .../6-libjson-glib-1.0-0_1.10.0+ds-3_armhf.deb ... 429s Unpacking libjson-glib-1.0-0:armhf (1.10.0+ds-3) over (1.10.0+ds-2) ... 429s Preparing to unpack .../7-libutempter0_1.2.1-4_armhf.deb ... 429s Unpacking libutempter0:armhf (1.2.1-4) over (1.2.1-3build1) ... 429s Setting up libnewt0.52:armhf (0.52.24-2ubuntu4) ... 429s Setting up libutempter0:armhf (1.2.1-4) ... 429s Setting up whiptail (0.52.24-2ubuntu4) ... 429s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 429s Setting up python3.13-gdbm (3.13.0-2) ... 429s Setting up libpython3-stdlib:armhf (3.12.7-1) ... 429s Setting up python3 (3.12.7-1) ... 429s Setting up python3-newt:armhf (0.52.24-2ubuntu4) ... 429s Setting up libjson-glib-1.0-0:armhf (1.10.0+ds-3) ... 429s Setting up python3-gdbm:armhf (3.12.7-1) ... 429s Processing triggers for man-db (2.12.1-3) ... 430s Processing triggers for libc-bin (2.40-1ubuntu3) ... 430s Reading package lists... 431s Building dependency tree... 431s Reading state information... 431s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 434s autopkgtest [21:30:40]: rebooting testbed after setup commands that affected boot 539s Reading package lists... 539s Building dependency tree... 539s Reading state information... 540s Starting pkgProblemResolver with broken count: 0 540s Starting 2 pkgProblemResolver with broken count: 0 540s Done 541s The following additional packages will be installed: 541s libaec0 libblas3 libgfortran5 libhdf5-103-1t64 libhdf5-hl-100t64 liblapack3 541s liblbfgsb0 liblzf1 libpython3.13-minimal libpython3.13-stdlib libsz2 541s python3-all python3-biom-format python3-click python3-colorama 541s python3-dateutil python3-decorator python3-h5py python3-h5py-serial 541s python3-numpy python3-pandas python3-pandas-lib python3-scipy python3-six 541s python3-tz python3.13 python3.13-minimal 541s Suggested packages: 541s python-biom-format-doc python-h5py-doc gcc gfortran python-numpy-doc 541s python3-dev python3-pytest python-pandas-doc python3-statsmodels 541s python-scipy-doc python3.13-venv python3.13-doc binfmt-support 541s Recommended packages: 541s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 541s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 541s g++ | c++-compiler python3-pil 541s The following NEW packages will be installed: 541s autopkgtest-satdep libaec0 libblas3 libgfortran5 libhdf5-103-1t64 541s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libpython3.13-minimal 541s libpython3.13-stdlib libsz2 python3-all python3-biom-format python3-click 541s python3-colorama python3-dateutil python3-decorator python3-h5py 541s python3-h5py-serial python3-numpy python3-pandas python3-pandas-lib 541s python3-scipy python3-six python3-tz python3.13 python3.13-minimal 541s 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. 541s Need to get 38.6 MB/38.6 MB of archives. 541s After this operation, 143 MB of additional disk space will be used. 541s Get:1 /tmp/autopkgtest.oPIwKo/2-autopkgtest-satdep.deb autopkgtest-satdep armhf 0 [724 B] 541s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-minimal armhf 3.13.0-2 [866 kB] 541s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13-minimal armhf 3.13.0-2 [1854 kB] 541s Get:4 http://ftpmaster.internal/ubuntu plucky/universe armhf libaec0 armhf 1.1.3-1 [20.8 kB] 541s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.0-3build2 [126 kB] 541s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 14.2.0-8ubuntu1 [311 kB] 541s Get:7 http://ftpmaster.internal/ubuntu plucky/universe armhf libsz2 armhf 1.1.3-1 [5302 B] 541s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-103-1t64 armhf 1.10.10+repack-4ubuntu3 [1327 kB] 542s Get:9 http://ftpmaster.internal/ubuntu plucky/universe armhf libhdf5-hl-100t64 armhf 1.10.10+repack-4ubuntu3 [55.9 kB] 542s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.0-3build2 [2086 kB] 542s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 542s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf liblzf1 armhf 3.6-4 [6554 B] 542s Get:13 http://ftpmaster.internal/ubuntu plucky/main armhf libpython3.13-stdlib armhf 3.13.0-2 [1972 kB] 542s Get:14 http://ftpmaster.internal/ubuntu plucky/main armhf python3.13 armhf 3.13.0-2 [719 kB] 542s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf python3-all armhf 3.12.7-1 [890 B] 542s Get:16 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:1.26.4+ds-11build1 [3570 kB] 542s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py-serial armhf 3.11.0-5ubuntu1 [1061 kB] 542s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-h5py all 3.11.0-5ubuntu1 [7974 B] 542s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf python3-colorama all 0.4.6-4 [32.1 kB] 542s Get:20 http://ftpmaster.internal/ubuntu plucky/main armhf python3-click all 8.1.7-2 [79.5 kB] 542s Get:21 http://ftpmaster.internal/ubuntu plucky/main armhf python3-six all 1.16.0-7 [13.1 kB] 542s Get:22 http://ftpmaster.internal/ubuntu plucky/main armhf python3-dateutil all 2.9.0-2 [80.3 kB] 542s Get:23 http://ftpmaster.internal/ubuntu plucky/main armhf python3-tz all 2024.1-2 [31.4 kB] 542s Get:24 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas-lib armhf 2.2.3+dfsg-5 [4728 kB] 542s Get:25 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pandas all 2.2.3+dfsg-5 [3112 kB] 542s Get:26 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 542s Get:27 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.13.1-5 [16.4 MB] 542s Get:28 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-biom-format armhf 2.1.16-1 [135 kB] 543s Fetched 38.6 MB in 2s (24.3 MB/s) 543s Selecting previously unselected package libpython3.13-minimal:armhf. 543s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 59567 files and directories currently installed.) 543s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_armhf.deb ... 543s Unpacking libpython3.13-minimal:armhf (3.13.0-2) ... 543s Selecting previously unselected package python3.13-minimal. 543s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_armhf.deb ... 543s Unpacking python3.13-minimal (3.13.0-2) ... 543s Selecting previously unselected package libaec0:armhf. 543s Preparing to unpack .../02-libaec0_1.1.3-1_armhf.deb ... 543s Unpacking libaec0:armhf (1.1.3-1) ... 543s Selecting previously unselected package libblas3:armhf. 543s Preparing to unpack .../03-libblas3_3.12.0-3build2_armhf.deb ... 543s Unpacking libblas3:armhf (3.12.0-3build2) ... 543s Selecting previously unselected package libgfortran5:armhf. 543s Preparing to unpack .../04-libgfortran5_14.2.0-8ubuntu1_armhf.deb ... 543s Unpacking libgfortran5:armhf (14.2.0-8ubuntu1) ... 543s Selecting previously unselected package libsz2:armhf. 543s Preparing to unpack .../05-libsz2_1.1.3-1_armhf.deb ... 543s Unpacking libsz2:armhf (1.1.3-1) ... 543s Selecting previously unselected package libhdf5-103-1t64:armhf. 543s Preparing to unpack .../06-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_armhf.deb ... 543s Unpacking libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 543s Selecting previously unselected package libhdf5-hl-100t64:armhf. 543s Preparing to unpack .../07-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_armhf.deb ... 543s Unpacking libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 543s Selecting previously unselected package liblapack3:armhf. 543s Preparing to unpack .../08-liblapack3_3.12.0-3build2_armhf.deb ... 543s Unpacking liblapack3:armhf (3.12.0-3build2) ... 543s Selecting previously unselected package liblbfgsb0:armhf. 543s Preparing to unpack .../09-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 543s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 543s Selecting previously unselected package liblzf1:armhf. 543s Preparing to unpack .../10-liblzf1_3.6-4_armhf.deb ... 543s Unpacking liblzf1:armhf (3.6-4) ... 543s Selecting previously unselected package libpython3.13-stdlib:armhf. 543s Preparing to unpack .../11-libpython3.13-stdlib_3.13.0-2_armhf.deb ... 543s Unpacking libpython3.13-stdlib:armhf (3.13.0-2) ... 543s Selecting previously unselected package python3.13. 544s Preparing to unpack .../12-python3.13_3.13.0-2_armhf.deb ... 544s Unpacking python3.13 (3.13.0-2) ... 544s 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up python3-decorator (5.1.1-5) ... 546s Setting up libblas3:armhf (3.12.0-3build2) ... 546s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 546s Setting up liblzf1:armhf (3.6-4) ... 546s Setting up libgfortran5:armhf (14.2.0-8ubuntu1) ... 546s Setting up python3.13-minimal (3.13.0-2) ... 547s Setting up python3-dateutil (2.9.0-2) ... 548s Setting up libpython3.13-stdlib:armhf (3.13.0-2) ... 548s Setting up libsz2:armhf (1.1.3-1) ... 548s Setting up liblapack3:armhf (3.12.0-3build2) ... 548s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 548s Setting up python3.13 (3.13.0-2) ... 549s Setting up python3-all (3.12.7-1) ... 549s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 553s Setting up libhdf5-103-1t64:armhf (1.10.10+repack-4ubuntu3) ... 553s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 553s Setting up libhdf5-hl-100t64:armhf (1.10.10+repack-4ubuntu3) ... 553s Setting up python3-scipy (1.13.1-5) ... 561s Setting up python3-pandas-lib:armhf (2.2.3+dfsg-5) ... 561s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ... 561s Setting up python3-pandas (2.2.3+dfsg-5) ... 572s Setting up python3-h5py (3.11.0-5ubuntu1) ... 572s Setting up python3-biom-format (2.1.16-1) ... 573s Setting up autopkgtest-satdep (0) ... 573s Processing triggers for systemd (256.5-2ubuntu4) ... 573s Processing triggers for man-db (2.12.1-3) ... 573s Processing triggers for libc-bin (2.40-1ubuntu3) ... 587s (Reading database ... 64717 files and directories currently installed.) 587s Removing autopkgtest-satdep (0) ... 601s autopkgtest [21:33:27]: 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 601s autopkgtest [21:33:27]: test autodep8-python3: [----------------------- 603s Testing with python3.13: 603s Traceback (most recent call last): 603s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 603s from . import multiarray 603s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 603s from . import overrides 603s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 603s from numpy.core._multiarray_umath import ( 603s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 603s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 603s 603s During handling of the above exception, another exception occurred: 603s 603s Traceback (most recent call last): 603s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 603s from numpy.__config__ import show as show_config 603s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 603s from numpy.core._multiarray_umath import ( 603s ...<3 lines>... 603s ) 603s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 603s raise ImportError(msg) 603s ImportError: 603s 603s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 603s 603s Importing the numpy C-extensions failed. This error can happen for 603s many reasons, often due to issues with your setup or how NumPy was 603s installed. 603s 603s We have compiled some common reasons and troubleshooting tips at: 603s 603s https://numpy.org/devdocs/user/troubleshooting-importerror.html 603s 603s Please note and check the following: 603s 603s * The Python version is: Python3.13 from "/usr/bin/python3.13" 603s * The NumPy version is: "1.26.4" 603s 603s and make sure that they are the versions you expect. 603s Please carefully study the documentation linked above for further help. 603s 603s Original error was: No module named 'numpy.core._multiarray_umath' 603s 603s 603s The above exception was the direct cause of the following exception: 603s 603s Traceback (most recent call last): 603s File "", line 1, in 603s import biom; print(biom) 603s ^^^^^^^^^^^ 603s File "/usr/lib/python3/dist-packages/biom/__init__.py", line 51, in 603s from .table import Table 603s File "/usr/lib/python3/dist-packages/biom/table.py", line 174, in 603s import numpy as np 603s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 603s raise ImportError(msg) from e 603s ImportError: Error importing numpy: you should not try to import numpy from 603s its source directory; please exit the numpy source tree, and relaunch 603s your python interpreter from there. 603s autopkgtest [21:33:29]: test autodep8-python3: -----------------------] 607s autopkgtest [21:33:33]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 607s autodep8-python3 FAIL non-zero exit status 1 611s autopkgtest [21:33:37]: @@@@@@@@@@@@@@@@@@@@ summary 611s run-unit-test PASS 611s autodep8-python3 FAIL non-zero exit status 1