0s autopkgtest [09:04:12]: starting date and time: 2024-07-08 09:04:12+0000 0s autopkgtest [09:04:12]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [09:04:12]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.clt4sp5x/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pandas --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=pandas/2.2.2+dfsg-4 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-10.secgroup --name adt-oracular-ppc64el-python-skbio-20240708-090352-juju-7f2275-prod-proposed-migration-environment-2-97cb2d5a-f435-44ef-bb76-23ce2c2315fb --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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://us.ports.ubuntu.com/ubuntu-ports/ 545s autopkgtest [09:13:17]: testbed dpkg architecture: ppc64el 545s autopkgtest [09:13:17]: testbed apt version: 2.9.6 545s autopkgtest [09:13:17]: @@@@@@@@@@@@@@@@@@@@ test bed setup 546s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 547s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 547s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [353 kB] 547s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [43.2 kB] 547s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 547s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [78.6 kB] 547s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2596 B] 547s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 547s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 547s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [335 kB] 547s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [9296 B] 547s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1448 B] 547s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 549s Fetched 962 kB in 1s (989 kB/s) 549s Reading package lists... 556s Reading package lists... 556s Building dependency tree... 556s Reading state information... 556s Calculating upgrade... 556s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 556s Reading package lists... 557s Building dependency tree... 557s Reading state information... 557s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 557s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 558s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 558s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 558s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 559s Reading package lists... 559s Reading package lists... 559s Building dependency tree... 559s Reading state information... 559s Calculating upgrade... 559s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 559s Reading package lists... 559s Building dependency tree... 559s Reading state information... 559s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 564s autopkgtest [09:13:36]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 564s autopkgtest [09:13:36]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 567s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (dsc) [2888 B] 567s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (tar) [2187 kB] 567s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (diff) [12.2 kB] 567s gpgv: Signature made Sat Jun 29 15:49:16 2024 UTC 567s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 567s gpgv: Can't check signature: No public key 567s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.6.1-2.dsc: no acceptable signature found 567s autopkgtest [09:13:39]: testing package python-skbio version 0.6.1-2 568s autopkgtest [09:13:40]: build not needed 573s autopkgtest [09:13:45]: test import-skbio: preparing testbed 575s Reading package lists... 575s Building dependency tree... 575s Reading state information... 575s Starting pkgProblemResolver with broken count: 0 575s Starting 2 pkgProblemResolver with broken count: 0 575s Done 576s The following additional packages will be installed: 576s libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 libhdf5-hl-100t64 576s liblapack3 liblbfgsb0 liblzf1 libssw0 libsz2 python3-biom-format 576s python3-click python3-colorama python3-dateutil python3-decorator 576s python3-h5py python3-h5py-serial python3-hdmedians python3-iniconfig 576s python3-natsort python3-numpy python3-packaging python3-pandas 576s python3-pandas-lib python3-pluggy python3-pytest python3-scipy python3-skbio 576s Suggested packages: 576s python-biom-format-doc python-h5py-doc python-natsort-doc gcc gfortran 576s python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 576s python-scipy-doc python-skbio-doc 576s Recommended packages: 576s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 576s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 576s g++ | c++-compiler python3-pil 576s The following NEW packages will be installed: 576s autopkgtest-satdep libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 576s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libssw0 libsz2 576s python3-biom-format python3-click python3-colorama python3-dateutil 576s python3-decorator python3-h5py python3-h5py-serial python3-hdmedians 576s python3-iniconfig python3-natsort python3-numpy python3-packaging 576s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 576s python3-scipy python3-skbio 576s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 576s Need to get 38.7 MB/38.7 MB of archives. 576s After this operation, 186 MB of additional disk space will be used. 576s Get:1 /tmp/autopkgtest.5PXmWr/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 576s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB] 576s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 576s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-1ubuntu1 [573 kB] 576s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgomp1 ppc64el 14.1.0-1ubuntu1 [161 kB] 576s Get:6 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B] 576s Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-3.1ubuntu4 [1395 kB] 577s Get:8 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-3.1ubuntu4 [70.9 kB] 577s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 577s Get:10 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 577s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B] 577s Get:12 http://ftpmaster.internal/ubuntu oracular/universe ppc64el libssw0 ppc64el 1.1-14build1 [24.5 kB] 577s Get:13 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 577s Get:14 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-h5py-serial ppc64el 3.10.0-1ubuntu3 [955 kB] 577s Get:15 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-h5py all 3.10.0-1ubuntu3 [7978 B] 577s Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-colorama all 0.4.6-4 [32.1 kB] 577s Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-click all 8.1.7-1 [79.1 kB] 577s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB] 577s Get:19 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-pandas-lib ppc64el 2.2.2+dfsg-4 [4602 kB] 577s Get:20 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-pandas all 2.2.2+dfsg-4 [3111 kB] 578s Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 578s Get:22 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-scipy ppc64el 1.12.0-2 [18.0 MB] 579s Get:23 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-biom-format ppc64el 2.1.16-1 [152 kB] 579s Get:24 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-hdmedians ppc64el 0.14.2-5.1build1 [147 kB] 579s Get:25 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 579s Get:26 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-natsort all 8.0.2-2 [33.8 kB] 579s Get:27 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.0-1 [41.1 kB] 579s Get:28 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 579s Get:29 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pytest all 7.4.4-1 [305 kB] 579s Get:30 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-skbio ppc64el 0.6.1-2 [1366 kB] 579s Fetched 38.7 MB in 3s (12.9 MB/s) 579s Selecting previously unselected package libaec0:ppc64el. 579s (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 ... 72746 files and directories currently installed.) 579s Preparing to unpack .../00-libaec0_1.1.3-1_ppc64el.deb ... 579s Unpacking libaec0:ppc64el (1.1.3-1) ... 579s Selecting previously unselected package libblas3:ppc64el. 579s Preparing to unpack .../01-libblas3_3.12.0-3build1_ppc64el.deb ... 579s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 579s Selecting previously unselected package libgfortran5:ppc64el. 579s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_ppc64el.deb ... 579s Unpacking libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 579s Selecting previously unselected package libgomp1:ppc64el. 579s Preparing to unpack .../03-libgomp1_14.1.0-1ubuntu1_ppc64el.deb ... 579s Unpacking libgomp1:ppc64el (14.1.0-1ubuntu1) ... 579s Selecting previously unselected package libsz2:ppc64el. 579s Preparing to unpack .../04-libsz2_1.1.3-1_ppc64el.deb ... 579s Unpacking libsz2:ppc64el (1.1.3-1) ... 579s Selecting previously unselected package libhdf5-103-1t64:ppc64el. 579s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_ppc64el.deb ... 579s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu4) ... 579s Selecting previously unselected package libhdf5-hl-100t64:ppc64el. 579s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_ppc64el.deb ... 579s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu4) ... 579s Selecting previously unselected package liblapack3:ppc64el. 579s Preparing to unpack .../07-liblapack3_3.12.0-3build1_ppc64el.deb ... 579s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 580s Selecting previously unselected package liblbfgsb0:ppc64el. 580s Preparing to unpack .../08-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 580s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 580s Selecting previously unselected package liblzf1:ppc64el. 580s Preparing to unpack .../09-liblzf1_3.6-4_ppc64el.deb ... 580s Unpacking liblzf1:ppc64el (3.6-4) ... 580s Selecting previously unselected package libssw0:ppc64el. 580s Preparing to unpack .../10-libssw0_1.1-14build1_ppc64el.deb ... 580s Unpacking libssw0:ppc64el (1.1-14build1) ... 580s Selecting previously unselected package python3-numpy. 580s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 580s Unpacking python3-numpy (1:1.26.4+ds-10) ... 580s Selecting previously unselected package python3-h5py-serial. 580s Preparing to unpack .../12-python3-h5py-serial_3.10.0-1ubuntu3_ppc64el.deb ... 580s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 580s Selecting previously unselected package python3-h5py. 580s Preparing to unpack .../13-python3-h5py_3.10.0-1ubuntu3_all.deb ... 580s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 580s Selecting previously unselected package python3-colorama. 580s Preparing to unpack .../14-python3-colorama_0.4.6-4_all.deb ... 580s Unpacking python3-colorama (0.4.6-4) ... 580s Selecting previously unselected package python3-click. 580s Preparing to unpack .../15-python3-click_8.1.7-1_all.deb ... 580s Unpacking python3-click (8.1.7-1) ... 580s Selecting previously unselected package python3-dateutil. 580s Preparing to unpack .../16-python3-dateutil_2.9.0-2_all.deb ... 580s Unpacking python3-dateutil (2.9.0-2) ... 580s Selecting previously unselected package python3-pandas-lib:ppc64el. 580s Preparing to unpack .../17-python3-pandas-lib_2.2.2+dfsg-4_ppc64el.deb ... 580s Unpacking python3-pandas-lib:ppc64el (2.2.2+dfsg-4) ... 580s Selecting previously unselected package python3-pandas. 580s Preparing to unpack .../18-python3-pandas_2.2.2+dfsg-4_all.deb ... 580s Unpacking python3-pandas (2.2.2+dfsg-4) ... 581s Selecting previously unselected package python3-decorator. 581s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 581s Unpacking python3-decorator (5.1.1-5) ... 581s Selecting previously unselected package python3-scipy. 581s Preparing to unpack .../20-python3-scipy_1.12.0-2_ppc64el.deb ... 581s Unpacking python3-scipy (1.12.0-2) ... 581s Selecting previously unselected package python3-biom-format. 581s Preparing to unpack .../21-python3-biom-format_2.1.16-1_ppc64el.deb ... 581s Unpacking python3-biom-format (2.1.16-1) ... 581s Selecting previously unselected package python3-hdmedians. 581s Preparing to unpack .../22-python3-hdmedians_0.14.2-5.1build1_ppc64el.deb ... 581s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 581s Selecting previously unselected package python3-iniconfig. 581s Preparing to unpack .../23-python3-iniconfig_1.1.1-2_all.deb ... 581s Unpacking python3-iniconfig (1.1.1-2) ... 581s Selecting previously unselected package python3-natsort. 581s Preparing to unpack .../24-python3-natsort_8.0.2-2_all.deb ... 581s Unpacking python3-natsort (8.0.2-2) ... 581s Selecting previously unselected package python3-packaging. 581s Preparing to unpack .../25-python3-packaging_24.0-1_all.deb ... 581s Unpacking python3-packaging (24.0-1) ... 581s Selecting previously unselected package python3-pluggy. 581s Preparing to unpack .../26-python3-pluggy_1.5.0-1_all.deb ... 581s Unpacking python3-pluggy (1.5.0-1) ... 581s Selecting previously unselected package python3-pytest. 581s Preparing to unpack .../27-python3-pytest_7.4.4-1_all.deb ... 581s Unpacking python3-pytest (7.4.4-1) ... 581s Selecting previously unselected package python3-skbio. 581s Preparing to unpack .../28-python3-skbio_0.6.1-2_ppc64el.deb ... 581s Unpacking python3-skbio (0.6.1-2) ... 582s Selecting previously unselected package autopkgtest-satdep. 582s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 582s Unpacking autopkgtest-satdep (0) ... 582s Setting up python3-iniconfig (1.1.1-2) ... 582s Setting up python3-colorama (0.4.6-4) ... 582s Setting up libgomp1:ppc64el (14.1.0-1ubuntu1) ... 582s Setting up python3-click (8.1.7-1) ... 582s Setting up libaec0:ppc64el (1.1.3-1) ... 582s Setting up python3-natsort (8.0.2-2) ... 582s Setting up python3-decorator (5.1.1-5) ... 582s Setting up libblas3:ppc64el (3.12.0-3build1) ... 582s 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 582s Setting up python3-packaging (24.0-1) ... 583s Setting up liblzf1:ppc64el (3.6-4) ... 583s Setting up libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 583s Setting up python3-pluggy (1.5.0-1) ... 583s Setting up python3-dateutil (2.9.0-2) ... 583s Setting up libssw0:ppc64el (1.1-14build1) ... 583s Setting up libsz2:ppc64el (1.1.3-1) ... 583s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 583s 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 583s Setting up python3-pytest (7.4.4-1) ... 583s Setting up python3-numpy (1:1.26.4+ds-10) ... 586s Setting up python3-hdmedians (0.14.2-5.1build1) ... 586s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-3.1ubuntu4) ... 586s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 586s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-3.1ubuntu4) ... 586s Setting up python3-scipy (1.12.0-2) ... 590s Setting up python3-pandas-lib:ppc64el (2.2.2+dfsg-4) ... 590s Setting up python3-h5py-serial (3.10.0-1ubuntu3) ... 590s Setting up python3-pandas (2.2.2+dfsg-4) ... 597s Setting up python3-h5py (3.10.0-1ubuntu3) ... 597s Setting up python3-biom-format (2.1.16-1) ... 597s Setting up python3-skbio (0.6.1-2) ... 598s Setting up autopkgtest-satdep (0) ... 598s Processing triggers for man-db (2.12.1-2) ... 599s Processing triggers for libc-bin (2.39-0ubuntu9) ... 602s (Reading database ... 78119 files and directories currently installed.) 602s Removing autopkgtest-satdep (0) ... 603s autopkgtest [09:14:15]: test import-skbio: [----------------------- 605s autopkgtest [09:14:17]: test import-skbio: -----------------------] 606s autopkgtest [09:14:18]: test import-skbio: - - - - - - - - - - results - - - - - - - - - - 606s import-skbio PASS 606s autopkgtest [09:14:18]: test testsuite: preparing testbed 608s Reading package lists... 608s Building dependency tree... 608s Reading state information... 608s Starting pkgProblemResolver with broken count: 0 608s Starting 2 pkgProblemResolver with broken count: 0 608s Done 608s The following NEW packages will be installed: 608s autopkgtest-satdep 608s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 608s Need to get 0 B/720 B of archives. 608s After this operation, 0 B of additional disk space will be used. 608s Get:1 /tmp/autopkgtest.5PXmWr/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 609s Selecting previously unselected package autopkgtest-satdep. 609s (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 ... 78119 files and directories currently installed.) 609s Preparing to unpack .../2-autopkgtest-satdep.deb ... 609s Unpacking autopkgtest-satdep (0) ... 609s Setting up autopkgtest-satdep (0) ... 611s (Reading database ... 78119 files and directories currently installed.) 611s Removing autopkgtest-satdep (0) ... 611s autopkgtest [09:14:23]: test testsuite: [----------------------- 612s + find . -name _hommola.py -exec sed -i /Run the cospeciation test with 99 permutations. Note that the correlation/,/After permuting host : parasite interactions, we find that the observed/d {} ; 612s + find . -name power.py -exec sed -i /Now, let's use random sampling to estimate the power of our test on/,/Based on this power estimate, as we increase our confidence that we have not/d {} ; 612s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 615s ============================= test session starts ============================== 615s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 615s rootdir: /tmp/autopkgtest.5PXmWr/autopkgtest_tmp 615s collected 2761 items 615s 616s skbio/alignment/tests/test_pairwise.py ......................... [ 0%] 616s skbio/alignment/tests/test_path.py ................. [ 1%] 616s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 616s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 616s ........................................................................ 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[ 85%] 681s skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%] 681s skbio/stats/ordination/tests/test_ordination_results.py .sssssssssss [ 86%] 682s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 86%] 682s ....... [ 86%] 682s skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 86%] 682s skbio/stats/ordination/tests/test_util.py .......... [ 87%] 682s skbio/stats/tests/test_composition.py .................................. [ 88%] 701s ................................................. [ 90%] 701s skbio/stats/tests/test_gradient.py .......................... [ 91%] 701s skbio/stats/tests/test_misc.py ... [ 91%] 704s skbio/stats/tests/test_power.py ........................................ [ 92%] 705s ... [ 92%] 707s skbio/stats/tests/test_subsample.py ............ [ 93%] 707s skbio/table/tests/test_base.py . [ 93%] 707s skbio/tests/test_base.py ..... [ 93%] 707s skbio/tests/test_workflow.py ................. [ 94%] 707s skbio/tree/tests/test_majority_rule.py ...... [ 94%] 707s skbio/tree/tests/test_nj.py ........... [ 94%] 707s skbio/tree/tests/test_tree.py .......................................... [ 96%] 707s ................................................... [ 98%] 707s skbio/util/tests/test_decorator.py ........ [ 98%] 707s skbio/util/tests/test_misc.py .................... [ 99%] 707s skbio/util/tests/test_plotting.py ssssss [ 99%] 707s skbio/util/tests/test_testing.py ............... [100%] 707s 707s =============================== warnings summary =============================== 707s skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/util/_warning.py:56: DeprecationWarning: make_identity_substitution_matrix is deprecated as of 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional details at https://github.com/scikit-bio/scikit-bio/pull/1913. 707s warn( 707s 707s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/util/_warning.py:56: DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It will be removed in favor of more general purpose and performant aligners. Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814. 707s warn( 707s 707s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 707s gap_freqs /= length 707s 707s skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/util/_warning.py:56: DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The return type is unstable. Developer caution is advised. The resulting DistanceMatrix object will include zeros when distance has not been calculated, and therefore can be misleading. 707s warn( 707s 707s skbio/metadata/tests/test_io.py: 10 warnings 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/metadata/io.py:411: FutureWarning: Downcasting behavior in `replace` is deprecated and will be removed in a future version. To retain the old behavior, explicitly call `result.infer_objects(copy=False)`. To opt-in to the future behavior, set `pd.set_option('future.no_silent_downcasting', True)` 707s series = series.replace("", np.nan) 707s 707s skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 707s skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 707s skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/metadata/_metadata.py:1102: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '['missing']' has dtype incompatible with float64, please explicitly cast to a compatible dtype first. 707s series[missing.index] = missing 707s 707s skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 707s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/metadata/tests/test_missing.py:53: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 707s pdt.assert_series_equal(missing, series.astype(object)) 707s 707s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 707s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/metadata/tests/test_missing.py:31: FutureWarning: Mismatched null-like values nan and None found. In a future version, pandas equality-testing functions (e.g. assert_frame_equal) will consider these not-matching and raise. 707s pdt.assert_series_equal(missing, series[1:].astype(object)) 707s 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 707s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 707s 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 707s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 707s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 707s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 707s 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 707s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 707s 707s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 707s obs_counts = obs_counts / len(self) 707s 707s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 707s warnings.warn(ConstantInputWarning()) 707s 707s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 707s warnings.warn(ConstantInputWarning()) 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.006573677549550482 and the largest is 0.17668321589384078. 707s warn( 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -13.541846544269617 and the largest is 16.587201374785895. 707s warn( 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -15.629533932395201 and the largest is 20.903154277938906. 707s warn( 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 707s proportion_explained = eigvals / sum_eigenvalues 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/distance/_permdisp.py:304: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 707s stat, _ = f_oneway(*groups) 707s 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 707s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:146: RuntimeWarning: The result contains negative eigenvalues. Please compare their magnitude with the magnitude of some of the largest positive eigenvalues. If the negative ones are smaller, it's probably safe to ignore them, but if they are large in magnitude, the results won't be useful. See the Notes section for more details. The smallest eigenvalue is -0.00775832514778062 and the largest is 2.7077929489469246. 707s warn( 707s 707s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 707s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 707s return self.run(*args, **kwds) 707s 707s skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 707s warn(f"{func.__name__} is deprecated as of {ver}.") 707s 707s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 707s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 707s res = hypotest_fun_out(*samples, **kwds) 707s 707s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 707s warn(f"{func.__name__} is deprecated as of {ver}.") 707s 707s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/composition.py:1654: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 707s return test(*[x[cats == k] for k in cs]) 707s 707s skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/composition.py:945: RuntimeWarning: divide by zero encountered in log 707s X_log = np.log(mat) 707s 707s skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 707s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 707s X -= avg[:, None] 707s 707s skbio/stats/tests/test_composition.py::VLRTests::test_vlr 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/composition.py:829: RuntimeWarning: divide by zero encountered in log 707s x = np.log(x) 707s 707s skbio/stats/tests/test_composition.py::VLRTests::test_vlr 707s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 707s x = asanyarray(arr - arrmean) 707s 707s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 707s /tmp/autopkgtest.5PXmWr/autopkgtest_tmp/skbio/stats/gradient.py:167: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise an error in a future version of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 707s trajectories.loc[idx] = ( 707s 707s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 707s ===== 2702 passed, 49 skipped, 10 xpassed, 66 warnings in 95.24s (0:01:35) ===== 708s autopkgtest [09:16:00]: test testsuite: -----------------------] 709s testsuite PASS 709s autopkgtest [09:16:01]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 709s autopkgtest [09:16:01]: @@@@@@@@@@@@@@@@@@@@ summary 709s import-skbio PASS 709s testsuite PASS 724s nova [W] Using flock in scalingstack-bos01-ppc64el 724s Creating nova instance adt-oracular-ppc64el-python-skbio-20240708-090352-juju-7f2275-prod-proposed-migration-environment-2-97cb2d5a-f435-44ef-bb76-23ce2c2315fb from image adt/ubuntu-oracular-ppc64el-server-20240708.img (UUID 5613d9b4-dcdb-4384-9080-3e8ed10c79bc)...