0s autopkgtest [09:02:13]: starting date and time: 2024-07-08 09:02:13+0000 0s autopkgtest [09:02:13]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [09:02:13]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.fh6atwd4/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@lcy02-86.secgroup --name adt-oracular-amd64-python-skbio-20240708-090213-juju-7f2275-prod-proposed-migration-environment-2-b7ac3673-1e82-4edd-a17a-44c61e954e6b --image adt/ubuntu-oracular-amd64-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://ftpmaster.internal/ubuntu/ 403s autopkgtest [09:08:56]: testbed dpkg architecture: amd64 403s autopkgtest [09:08:56]: testbed apt version: 2.9.6 403s autopkgtest [09:08:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 405s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 405s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 405s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [43.2 kB] 405s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 405s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [353 kB] 405s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [101 kB] 405s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [74.0 kB] 405s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 c-n-f Metadata [2592 B] 405s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [34.9 kB] 405s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [6244 B] 405s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 c-n-f Metadata [368 B] 405s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [345 kB] 405s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [199 kB] 405s Get:14 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 c-n-f Metadata [9628 B] 405s Get:15 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [7644 B] 405s Get:16 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3052 B] 405s Get:17 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 c-n-f Metadata [276 B] 406s Fetched 1317 kB in 0s (4732 kB/s) 406s Reading package lists... 410s Reading package lists... 410s Building dependency tree... 410s Reading state information... 410s Calculating upgrade... 411s The following packages will be upgraded: 411s fuse3 libfuse3-3 411s 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 411s Need to get 109 kB of archives. 411s After this operation, 4096 B of additional disk space will be used. 411s Get:1 http://ftpmaster.internal/ubuntu oracular/main amd64 fuse3 amd64 3.14.0-6 [25.5 kB] 411s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libfuse3-3 amd64 3.14.0-6 [83.2 kB] 411s Fetched 109 kB in 0s (4671 kB/s) 411s (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 ... 74464 files and directories currently installed.) 444s Preparing to unpack .../fuse3_3.14.0-6_amd64.deb ... 444s Adding 'diversion of /bin/fusermount to /bin/fusermount.usr-is-merged by fuse3' 444s Adding 'diversion of /sbin/mount.fuse to /sbin/mount.fuse.usr-is-merged by fuse3' 444s Unpacking fuse3 (3.14.0-6) over (3.14.0-5build1) ... 444s Preparing to unpack .../libfuse3-3_3.14.0-6_amd64.deb ... 444s Unpacking libfuse3-3:amd64 (3.14.0-6) over (3.14.0-5build1) ... 444s Setting up libfuse3-3:amd64 (3.14.0-6) ... 444s Setting up fuse3 (3.14.0-6) ... 444s Removing 'diversion of /bin/fusermount to /bin/fusermount.usr-is-merged by fuse3' 444s Removing 'diversion of /sbin/mount.fuse to /sbin/mount.fuse.usr-is-merged by fuse3' 444s update-initramfs: deferring update (trigger activated) 444s Processing triggers for libc-bin (2.39-0ubuntu9) ... 444s Processing triggers for man-db (2.12.1-2) ... 444s Processing triggers for initramfs-tools (0.142ubuntu29) ... 444s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 444s Get:2 http://ftpmaster.internal/ubuntu oracular InRelease [121 kB] 444s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 444s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 444s update-initramfs: Generating /boot/initrd.img-6.8.0-31-generic 444s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 444s Reading package lists... 444s Building dependency tree... 444s Reading state information... 444s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 444s Reading package lists... 444s Building dependency tree... 444s Reading state information... 444s Calculating upgrade... 444s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 444s Reading package lists... 444s Building dependency tree... 444s Reading state information... 444s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 444s Get:5 http://ftpmaster.internal/ubuntu oracular/universe Sources [20.3 MB] 444s Get:6 http://ftpmaster.internal/ubuntu oracular/universe i386 Packages [8739 kB] 444s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 Packages [15.8 MB] 444s Fetched 44.9 MB in 4s (12.7 MB/s) 444s Reading package lists... 444s autopkgtest [09:09:21]: rebooting testbed after setup commands that affected boot 461s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 498s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 504s autopkgtest [09:10:37]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 558s autopkgtest [09:11:31]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 592s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (dsc) [2888 B] 592s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (tar) [2187 kB] 592s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.6.1-2 (diff) [12.2 kB] 593s gpgv: Signature made Sat Jun 29 15:49:16 2024 UTC 593s gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 593s gpgv: Can't check signature: No public key 593s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.6.1-2.dsc: no acceptable signature found 593s autopkgtest [09:12:06]: testing package python-skbio version 0.6.1-2 593s autopkgtest [09:12:06]: build not needed 593s autopkgtest [09:12:06]: test import-skbio: preparing testbed 594s Reading package lists... 594s Building dependency tree... 594s Reading state information... 594s Starting pkgProblemResolver with broken count: 0 594s Starting 2 pkgProblemResolver with broken count: 0 594s Done 595s The following additional packages will be installed: 595s libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 libhdf5-hl-100t64 595s liblapack3 liblbfgsb0 liblzf1 libssw0 libsz2 python3-biom-format 595s python3-click python3-colorama python3-dateutil python3-decorator 595s python3-h5py python3-h5py-serial python3-hdmedians python3-iniconfig 595s python3-natsort python3-numpy python3-packaging python3-pandas 595s python3-pandas-lib python3-pluggy python3-pytest python3-scipy python3-skbio 595s Suggested packages: 595s python-biom-format-doc python-h5py-doc python-natsort-doc gcc gfortran 595s python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 595s python-scipy-doc python-skbio-doc 595s Recommended packages: 595s python3-matplotlib python3-bottleneck python3-numexpr python3-odf 595s python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables 595s python3-numba g++ | c++-compiler python3-pil 595s The following NEW packages will be installed: 595s autopkgtest-satdep libaec0 libblas3 libgfortran5 libgomp1 libhdf5-103-1t64 595s libhdf5-hl-100t64 liblapack3 liblbfgsb0 liblzf1 libssw0 libsz2 595s python3-biom-format python3-click python3-colorama python3-dateutil 595s python3-decorator python3-h5py python3-h5py-serial python3-hdmedians 595s python3-iniconfig python3-natsort python3-numpy python3-packaging 595s python3-pandas python3-pandas-lib python3-pluggy python3-pytest 595s python3-scipy python3-skbio 595s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 595s Need to get 37.0 MB/37.0 MB of archives. 595s After this operation, 166 MB of additional disk space will be used. 595s Get:1 /tmp/autopkgtest.9oMo6d/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 595s Get:2 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 595s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 595s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 595s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 595s Get:6 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 595s Get:7 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 595s Get:8 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.1ubuntu4 [56.0 kB] 595s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 595s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 595s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 595s Get:12 http://ftpmaster.internal/ubuntu oracular/universe amd64 libssw0 amd64 1.1-14build1 [22.1 kB] 595s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 595s Get:14 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu3 [906 kB] 595s Get:15 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 595s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-colorama all 0.4.6-4 [32.1 kB] 595s Get:17 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-click all 8.1.7-1 [79.1 kB] 595s Get:18 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 595s Get:19 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pandas-lib amd64 2.2.2+dfsg-4 [4444 kB] 595s Get:20 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pandas all 2.2.2+dfsg-4 [3111 kB] 595s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 595s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.12.0-2 [16.5 MB] 595s Get:23 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-biom-format amd64 2.1.16-1 [141 kB] 595s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-hdmedians amd64 0.14.2-5.1build1 [124 kB] 595s Get:25 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 595s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 595s Get:27 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 595s Get:28 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 595s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pytest all 7.4.4-1 [305 kB] 595s Get:30 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-skbio amd64 0.6.1-2 [1333 kB] 595s Fetched 37.0 MB in 0s (131 MB/s) 595s Selecting previously unselected package libaec0:amd64. 596s (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 ... 74466 files and directories currently installed.) 596s Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... 596s Unpacking libaec0:amd64 (1.1.3-1) ... 596s Selecting previously unselected package libblas3:amd64. 596s Preparing to unpack .../01-libblas3_3.12.0-3build1_amd64.deb ... 596s Unpacking libblas3:amd64 (3.12.0-3build1) ... 596s Selecting previously unselected package libgfortran5:amd64. 596s Preparing to unpack .../02-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 596s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 596s Selecting previously unselected package libgomp1:amd64. 596s Preparing to unpack .../03-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 596s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 596s Selecting previously unselected package libsz2:amd64. 596s Preparing to unpack .../04-libsz2_1.1.3-1_amd64.deb ... 596s Unpacking libsz2:amd64 (1.1.3-1) ... 596s Selecting previously unselected package libhdf5-103-1t64:amd64. 596s Preparing to unpack .../05-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 596s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 596s Selecting previously unselected package libhdf5-hl-100t64:amd64. 596s Preparing to unpack .../06-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 596s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 596s Selecting previously unselected package liblapack3:amd64. 596s Preparing to unpack .../07-liblapack3_3.12.0-3build1_amd64.deb ... 596s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 596s Selecting previously unselected package liblbfgsb0:amd64. 596s Preparing to unpack .../08-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 596s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 596s Selecting previously unselected package liblzf1:amd64. 596s Preparing to unpack .../09-liblzf1_3.6-4_amd64.deb ... 596s Unpacking liblzf1:amd64 (3.6-4) ... 596s Selecting previously unselected package libssw0:amd64. 596s Preparing to unpack .../10-libssw0_1.1-14build1_amd64.deb ... 596s Unpacking libssw0:amd64 (1.1-14build1) ... 596s Selecting previously unselected package python3-numpy. 596s Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 596s Unpacking python3-numpy (1:1.26.4+ds-10) ... 596s Selecting previously unselected package python3-h5py-serial. 596s Preparing to unpack .../12-python3-h5py-serial_3.10.0-1ubuntu3_amd64.deb ... 596s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 596s Selecting previously unselected package python3-h5py. 596s Preparing to unpack .../13-python3-h5py_3.10.0-1ubuntu3_all.deb ... 596s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 596s Selecting previously unselected package python3-colorama. 596s Preparing to unpack .../14-python3-colorama_0.4.6-4_all.deb ... 596s Unpacking python3-colorama (0.4.6-4) ... 596s Selecting previously unselected package python3-click. 596s Preparing to unpack .../15-python3-click_8.1.7-1_all.deb ... 596s Unpacking python3-click (8.1.7-1) ... 596s Selecting previously unselected package python3-dateutil. 596s Preparing to unpack .../16-python3-dateutil_2.9.0-2_all.deb ... 596s Unpacking python3-dateutil (2.9.0-2) ... 596s Selecting previously unselected package python3-pandas-lib:amd64. 596s Preparing to unpack .../17-python3-pandas-lib_2.2.2+dfsg-4_amd64.deb ... 596s Unpacking python3-pandas-lib:amd64 (2.2.2+dfsg-4) ... 596s Selecting previously unselected package python3-pandas. 596s Preparing to unpack .../18-python3-pandas_2.2.2+dfsg-4_all.deb ... 596s Unpacking python3-pandas (2.2.2+dfsg-4) ... 597s Selecting previously unselected package python3-decorator. 597s Preparing to unpack .../19-python3-decorator_5.1.1-5_all.deb ... 597s Unpacking python3-decorator (5.1.1-5) ... 597s Selecting previously unselected package python3-scipy. 597s Preparing to unpack .../20-python3-scipy_1.12.0-2_amd64.deb ... 597s Unpacking python3-scipy (1.12.0-2) ... 597s Selecting previously unselected package python3-biom-format. 597s Preparing to unpack .../21-python3-biom-format_2.1.16-1_amd64.deb ... 597s Unpacking python3-biom-format (2.1.16-1) ... 597s Selecting previously unselected package python3-hdmedians. 597s Preparing to unpack .../22-python3-hdmedians_0.14.2-5.1build1_amd64.deb ... 597s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 597s Selecting previously unselected package python3-iniconfig. 597s Preparing to unpack .../23-python3-iniconfig_1.1.1-2_all.deb ... 597s Unpacking python3-iniconfig (1.1.1-2) ... 597s Selecting previously unselected package python3-natsort. 597s Preparing to unpack .../24-python3-natsort_8.0.2-2_all.deb ... 597s Unpacking python3-natsort (8.0.2-2) ... 597s Selecting previously unselected package python3-packaging. 597s Preparing to unpack .../25-python3-packaging_24.0-1_all.deb ... 597s Unpacking python3-packaging (24.0-1) ... 597s Selecting previously unselected package python3-pluggy. 597s Preparing to unpack .../26-python3-pluggy_1.5.0-1_all.deb ... 597s Unpacking python3-pluggy (1.5.0-1) ... 597s Selecting previously unselected package python3-pytest. 597s Preparing to unpack .../27-python3-pytest_7.4.4-1_all.deb ... 597s Unpacking python3-pytest (7.4.4-1) ... 597s Selecting previously unselected package python3-skbio. 597s Preparing to unpack .../28-python3-skbio_0.6.1-2_amd64.deb ... 597s Unpacking python3-skbio (0.6.1-2) ... 598s Selecting previously unselected package autopkgtest-satdep. 598s Preparing to unpack .../29-1-autopkgtest-satdep.deb ... 598s Unpacking autopkgtest-satdep (0) ... 598s Setting up python3-iniconfig (1.1.1-2) ... 598s Setting up python3-colorama (0.4.6-4) ... 598s Setting up libgomp1:amd64 (14.1.0-1ubuntu1) ... 598s Setting up python3-click (8.1.7-1) ... 598s Setting up libaec0:amd64 (1.1.3-1) ... 598s Setting up python3-natsort (8.0.2-2) ... 598s Setting up python3-decorator (5.1.1-5) ... 598s Setting up libblas3:amd64 (3.12.0-3build1) ... 598s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 598s Setting up python3-packaging (24.0-1) ... 598s Setting up liblzf1:amd64 (3.6-4) ... 598s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 598s Setting up python3-pluggy (1.5.0-1) ... 599s Setting up python3-dateutil (2.9.0-2) ... 599s Setting up libssw0:amd64 (1.1-14build1) ... 599s Setting up libsz2:amd64 (1.1.3-1) ... 599s Setting up liblapack3:amd64 (3.12.0-3build1) ... 599s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 599s Setting up python3-pytest (7.4.4-1) ... 599s Setting up python3-numpy (1:1.26.4+ds-10) ... 601s Setting up python3-hdmedians (0.14.2-5.1build1) ... 601s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 601s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 601s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 601s Setting up python3-scipy (1.12.0-2) ... 604s Setting up python3-pandas-lib:amd64 (2.2.2+dfsg-4) ... 604s Setting up python3-h5py-serial (3.10.0-1ubuntu3) ... 605s Setting up python3-pandas (2.2.2+dfsg-4) ... 610s Setting up python3-h5py (3.10.0-1ubuntu3) ... 610s Setting up python3-biom-format (2.1.16-1) ... 610s Setting up python3-skbio (0.6.1-2) ... 611s Setting up autopkgtest-satdep (0) ... 611s Processing triggers for man-db (2.12.1-2) ... 612s Processing triggers for libc-bin (2.39-0ubuntu9) ... 619s (Reading database ... 79839 files and directories currently installed.) 619s Removing autopkgtest-satdep (0) ... 619s autopkgtest [09:12:32]: test import-skbio: [----------------------- 621s autopkgtest [09:12:34]: test import-skbio: -----------------------] 622s autopkgtest [09:12:35]: test import-skbio: - - - - - - - - - - results - - - - - - - - - - 622s import-skbio PASS 622s autopkgtest [09:12:35]: test testsuite: preparing testbed 623s Reading package lists... 623s Building dependency tree... 623s Reading state information... 624s Starting pkgProblemResolver with broken count: 0 624s Starting 2 pkgProblemResolver with broken count: 0 624s Done 625s The following NEW packages will be installed: 625s autopkgtest-satdep 625s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 625s Need to get 0 B/716 B of archives. 625s After this operation, 0 B of additional disk space will be used. 625s Get:1 /tmp/autopkgtest.9oMo6d/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 625s Selecting previously unselected package autopkgtest-satdep. 625s (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 ... 79839 files and directories currently installed.) 625s Preparing to unpack .../2-autopkgtest-satdep.deb ... 625s Unpacking autopkgtest-satdep (0) ... 625s Setting up autopkgtest-satdep (0) ... 627s (Reading database ... 79839 files and directories currently installed.) 627s Removing autopkgtest-satdep (0) ... 628s autopkgtest [09:12:41]: test testsuite: [----------------------- 628s + 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 {} ; 628s + 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 {} ; 628s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 631s ============================= test session starts ============================== 631s platform linux -- Python 3.12.4, pytest-7.4.4, pluggy-1.5.0 631s rootdir: /tmp/autopkgtest.9oMo6d/autopkgtest_tmp 631s collected 2761 items 631s 631s skbio/alignment/tests/test_pairwise.py ......................... [ 0%] 631s skbio/alignment/tests/test_path.py ................. [ 1%] 631s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 631s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 632s ........................................................................ 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[ 85%] 700s skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 85%] 700s skbio/stats/ordination/tests/test_ordination_results.py .sssssssssss [ 86%] 700s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 86%] 700s ....... [ 86%] 701s skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 86%] 701s skbio/stats/ordination/tests/test_util.py .......... [ 87%] 701s skbio/stats/tests/test_composition.py .................................. [ 88%] 715s ................................................. [ 90%] 715s skbio/stats/tests/test_gradient.py .......................... [ 91%] 715s skbio/stats/tests/test_misc.py ... [ 91%] 717s skbio/stats/tests/test_power.py ........................................ [ 92%] 717s ... [ 92%] 719s skbio/stats/tests/test_subsample.py ............ [ 93%] 719s skbio/table/tests/test_base.py . [ 93%] 719s skbio/tests/test_base.py ..... [ 93%] 719s skbio/tests/test_workflow.py ................. [ 94%] 719s skbio/tree/tests/test_majority_rule.py ...... [ 94%] 719s skbio/tree/tests/test_nj.py ........... [ 94%] 719s skbio/tree/tests/test_tree.py .......................................... [ 96%] 719s ................................................... [ 98%] 719s skbio/util/tests/test_decorator.py ........ [ 98%] 719s skbio/util/tests/test_misc.py .................... [ 99%] 719s skbio/util/tests/test_plotting.py ssssss [ 99%] 719s skbio/util/tests/test_testing.py ............... [100%] 719s 719s =============================== warnings summary =============================== 719s skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices 719s /tmp/autopkgtest.9oMo6d/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. 719s warn( 719s 719s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 719s /tmp/autopkgtest.9oMo6d/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. 719s warn( 719s 719s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1648: RuntimeWarning: invalid value encountered in divide 719s gap_freqs /= length 719s 719s skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity 719s /tmp/autopkgtest.9oMo6d/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. 719s warn( 719s 719s skbio/metadata/tests/test_io.py: 10 warnings 719s /tmp/autopkgtest.9oMo6d/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)` 719s series = series.replace("", np.nan) 719s 719s skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing 719s skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true 719s skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true 719s /tmp/autopkgtest.9oMo6d/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. 719s series[missing.index] = missing 719s 719s skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object 719s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object 719s /tmp/autopkgtest.9oMo6d/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. 719s pdt.assert_series_equal(missing, series.astype(object)) 719s 719s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool 719s skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string 719s /tmp/autopkgtest.9oMo6d/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. 719s pdt.assert_series_equal(missing, series[1:].astype(object)) 719s 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:639: DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 719s warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) 719s 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 719s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 719s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:313: DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 719s warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) 719s 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/sequence/_grammared_sequence.py:572: DeprecationWarning: nondenengerates is deprecated as of 0.5.0. 719s warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) 719s 719s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/sequence/_sequence.py:1824: RuntimeWarning: invalid value encountered in divide 719s obs_counts = obs_counts / len(self) 719s 719s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/distance/_mantel.py:364: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 719s warnings.warn(ConstantInputWarning()) 719s 719s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/distance/_mantel.py:483: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 719s warnings.warn(ConstantInputWarning()) 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series 719s /tmp/autopkgtest.9oMo6d/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 -0.006573677549550485 and the largest is 0.17668321589384078. 719s warn( 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 719s /tmp/autopkgtest.9oMo6d/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 -13.54184654426961 and the largest is 16.5872013747859. 719s warn( 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 719s /tmp/autopkgtest.9oMo6d/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 -15.629533932395208 and the largest is 20.90315427793891. 719s warn( 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:190: RuntimeWarning: invalid value encountered in divide 719s proportion_explained = eigvals / sum_eigenvalues 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/distance/_permdisp.py:304: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 719s stat, _ = f_oneway(*groups) 719s 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 719s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 719s /tmp/autopkgtest.9oMo6d/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 -0.007758325147780521 and the largest is 2.7077929489469237. 719s warn( 719s 719s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 719s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 719s return self.run(*args, **kwds) 719s 719s skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/util/_warning.py:60: UserWarning: multiplicative_replacement is deprecated as of 0.6.0. 719s warn(f"{func.__name__} is deprecated as of {ver}.") 719s 719s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 719s /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. 719s res = hypotest_fun_out(*samples, **kwds) 719s 719s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/util/_warning.py:60: UserWarning: ancom is deprecated as of 0.6.0. 719s warn(f"{func.__name__} is deprecated as of {ver}.") 719s 719s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/composition.py:1654: ConstantInputWarning: Each of the input arrays is constant; the F statistic is not defined or infinite 719s return test(*[x[cats == k] for k in cs]) 719s 719s skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/composition.py:945: RuntimeWarning: divide by zero encountered in log 719s X_log = np.log(mat) 719s 719s skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr 719s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 719s X -= avg[:, None] 719s 719s skbio/stats/tests/test_composition.py::VLRTests::test_vlr 719s /tmp/autopkgtest.9oMo6d/autopkgtest_tmp/skbio/stats/composition.py:829: RuntimeWarning: divide by zero encountered in log 719s x = np.log(x) 719s 719s skbio/stats/tests/test_composition.py::VLRTests::test_vlr 719s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 719s x = asanyarray(arr - arrmean) 719s 719s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 719s /tmp/autopkgtest.9oMo6d/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. 719s trajectories.loc[idx] = ( 719s 719s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 719s ===== 2702 passed, 49 skipped, 10 xpassed, 66 warnings in 91.43s (0:01:31) ===== 721s autopkgtest [09:14:14]: test testsuite: -----------------------] 721s testsuite PASS 721s autopkgtest [09:14:14]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 721s autopkgtest [09:14:14]: @@@@@@@@@@@@@@@@@@@@ summary 721s import-skbio PASS 721s testsuite PASS 734s nova [W] Skipping flock for amd64 734s Creating nova instance adt-oracular-amd64-python-skbio-20240708-090213-juju-7f2275-prod-proposed-migration-environment-2-b7ac3673-1e82-4edd-a17a-44c61e954e6b from image adt/ubuntu-oracular-amd64-server-20240707.img (UUID a564d08f-b120-4297-9fe1-fa5551c3a09b)...