0s autopkgtest [00:25:09]: starting date and time: 2024-06-08 00:25:09+0000 0s autopkgtest [00:25:09]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [00:25:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2eq_lr06/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-90.secgroup --name adt-oracular-amd64-python-skbio-20240608-002508-juju-7f2275-prod-proposed-migration-environment-2-7a84b354-8785-4b66-8c16-de5e7bf2996d --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/ 123s autopkgtest [00:27:12]: testbed dpkg architecture: amd64 123s autopkgtest [00:27:12]: testbed apt version: 2.9.3 123s autopkgtest [00:27:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup 124s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 124s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [339 kB] 124s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 124s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 124s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2852 B] 124s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main i386 Packages [37.8 kB] 124s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main amd64 Packages [65.6 kB] 124s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted amd64 Packages [27.4 kB] 124s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted i386 Packages [9340 B] 124s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe i386 Packages [124 kB] 124s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 Packages [300 kB] 124s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse amd64 Packages [9280 B] 124s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse i386 Packages [3368 B] 124s Fetched 1081 kB in 0s (3943 kB/s) 124s Reading package lists... 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Calculating upgrade... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 127s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 127s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 127s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 127s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 129s Reading package lists... 129s Reading package lists... 129s Building dependency tree... 129s Reading state information... 129s Calculating upgrade... 129s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s Reading package lists... 130s Building dependency tree... 130s Reading state information... 130s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 131s autopkgtest [00:27:20]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 00:40:06 UTC 2024 131s autopkgtest [00:27:20]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 132s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (dsc) [2803 B] 132s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (tar) [3559 kB] 132s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (diff) [15.7 kB] 132s gpgv: Signature made Wed Apr 10 15:30:06 2024 UTC 132s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4build1.dsc: no acceptable signature found 132s autopkgtest [00:27:21]: testing package python-skbio version 0.5.9-4build1 132s autopkgtest [00:27:21]: build not needed 133s autopkgtest [00:27:22]: test import-skbio: preparing testbed 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 134s Starting pkgProblemResolver with broken count: 0 134s Starting 2 pkgProblemResolver with broken count: 0 134s Done 134s The following additional packages will be installed: 134s blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 libgraphite2-3 134s libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjs-jquery 134s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libopenjp2-7 134s libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 134s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 134s python3-appdirs python3-asttokens python3-brotli python3-contourpy 134s python3-cycler python3-dateutil python3-decorator python3-executing 134s python3-fonttools python3-fs python3-h5py python3-h5py-serial 134s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 134s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 134s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 134s python3-packaging python3-pandas python3-pandas-lib python3-parso 134s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 134s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 134s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 134s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 134s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 134s Suggested packages: 134s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 134s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 134s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 134s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 134s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 134s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 134s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 134s python-pexpect-doc python-pil-doc python-scipy-doc python-skbio-doc 134s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 134s Recommended packages: 134s javascript-common python3-bs4 python3-cssselect python3-html5lib 134s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 134s python3-tables python3-numba python3-olefile g++ | c++-compiler 134s isympy-common 134s The following NEW packages will be installed: 134s autopkgtest-satdep blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 134s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 134s libimagequant0 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 134s liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 134s libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 134s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 134s python3-contourpy python3-cycler python3-dateutil python3-decorator 134s python3-executing python3-fonttools python3-fs python3-h5py 134s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 134s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 134s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 134s python3-packaging python3-pandas python3-pandas-lib python3-parso 134s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 134s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 134s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 134s python3-traitlets python3-typeshed python3-ufolib2 python3-unicodedata2 134s python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 134s 0 upgraded, 81 newly installed, 0 to remove and 0 not upgraded. 134s Need to get 69.4 MB/69.4 MB of archives. 134s After this operation, 315 MB of additional disk space will be used. 134s Get:1 /tmp/autopkgtest.hddjcZ/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 134s Get:2 http://ftpmaster.internal/ubuntu oracular/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1build1 [988 kB] 134s Get:3 http://ftpmaster.internal/ubuntu oracular/main amd64 libxrender1 amd64 1:0.9.10-1.1build1 [19.0 kB] 134s Get:4 http://ftpmaster.internal/ubuntu oracular/main amd64 libxft2 amd64 2.3.6-1build1 [45.3 kB] 134s Get:5 http://ftpmaster.internal/ubuntu oracular/main amd64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 134s Get:6 http://ftpmaster.internal/ubuntu oracular/main amd64 libxss1 amd64 1:1.2.3-1build3 [7204 B] 134s Get:7 http://ftpmaster.internal/ubuntu oracular/main amd64 libtk8.6 amd64 8.6.14-1build1 [779 kB] 134s Get:8 http://ftpmaster.internal/ubuntu oracular/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7build1 [630 kB] 134s Get:9 http://ftpmaster.internal/ubuntu oracular/main amd64 blt amd64 2.5.3+dfsg-7build1 [4840 B] 134s Get:10 http://ftpmaster.internal/ubuntu oracular/universe amd64 fonts-lyx all 2.4.0-1 [171 kB] 134s Get:11 http://ftpmaster.internal/ubuntu oracular/universe amd64 libaec0 amd64 1.1.3-1 [22.7 kB] 134s Get:12 http://ftpmaster.internal/ubuntu oracular/main amd64 libblas3 amd64 3.12.0-3build1 [238 kB] 134s Get:13 http://ftpmaster.internal/ubuntu oracular/main amd64 libgfortran5 amd64 14.1.0-1ubuntu1 [928 kB] 134s Get:14 http://ftpmaster.internal/ubuntu oracular/main amd64 libgomp1 amd64 14.1.0-1ubuntu1 [148 kB] 134s Get:15 http://ftpmaster.internal/ubuntu oracular/main amd64 libgraphite2-3 amd64 1.3.14-2build1 [73.0 kB] 134s Get:16 http://ftpmaster.internal/ubuntu oracular/main amd64 libharfbuzz0b amd64 8.3.0-2build2 [469 kB] 134s Get:17 http://ftpmaster.internal/ubuntu oracular/universe amd64 libsz2 amd64 1.1.3-1 [5456 B] 134s Get:18 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1ubuntu4 [1270 kB] 134s Get:19 http://ftpmaster.internal/ubuntu oracular/universe amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.1ubuntu4 [56.0 kB] 134s Get:20 http://ftpmaster.internal/ubuntu oracular/main amd64 libimagequant0 amd64 2.18.0-1build1 [36.3 kB] 134s Get:21 http://ftpmaster.internal/ubuntu oracular/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 134s Get:22 http://ftpmaster.internal/ubuntu oracular/universe amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 134s Get:23 http://ftpmaster.internal/ubuntu oracular/main amd64 liblapack3 amd64 3.12.0-3build1 [2650 kB] 134s Get:24 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 134s Get:25 http://ftpmaster.internal/ubuntu oracular/main amd64 liblcms2-2 amd64 2.14-2build1 [161 kB] 134s Get:26 http://ftpmaster.internal/ubuntu oracular/universe amd64 liblzf1 amd64 3.6-4 [7624 B] 134s Get:27 http://ftpmaster.internal/ubuntu oracular/universe amd64 libqhull-r8.0 amd64 2020.2-6build1 [193 kB] 134s Get:28 http://ftpmaster.internal/ubuntu oracular/main amd64 libraqm0 amd64 0.10.1-1build1 [15.0 kB] 134s Get:29 http://ftpmaster.internal/ubuntu oracular/universe amd64 libssw0 amd64 1.1-14build1 [22.1 kB] 134s Get:30 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpdemux2 amd64 1.4.0-0.1 [12.4 kB] 134s Get:31 http://ftpmaster.internal/ubuntu oracular/main amd64 libwebpmux3 amd64 1.4.0-0.1 [25.8 kB] 134s Get:32 http://ftpmaster.internal/ubuntu oracular/main amd64 libxslt1.1 amd64 1.1.39-0exp1build1 [167 kB] 134s Get:33 http://ftpmaster.internal/ubuntu oracular/universe amd64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 134s Get:34 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-appdirs all 1.4.4-4 [10.9 kB] 134s Get:35 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-asttokens all 2.4.1-1 [20.9 kB] 134s Get:36 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-brotli amd64 1.1.0-2build2 [332 kB] 134s Get:37 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-numpy amd64 1:1.26.4+ds-10 [4437 kB] 134s Get:38 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-contourpy amd64 1.0.7-3 [181 kB] 134s Get:39 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-cycler all 0.12.1-1 [9716 B] 134s Get:40 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-dateutil all 2.9.0-2 [80.3 kB] 134s Get:41 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 134s Get:42 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-executing all 2.0.1-0.1 [23.3 kB] 134s Get:43 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-scipy amd64 1.11.4-10 [15.5 MB] 134s Get:44 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 134s Get:45 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-mpmath all 1.3.0-1 [425 kB] 134s Get:46 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-sympy all 1.12-8 [3966 kB] 134s Get:47 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fs all 2.4.16-4 [91.3 kB] 134s Get:48 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-lxml amd64 5.2.1-1 [1243 kB] 134s Get:49 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-lz4 amd64 4.0.2+dfsg-1build4 [26.2 kB] 134s Get:50 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-unicodedata2 amd64 15.1.0+ds-1build1 [362 kB] 134s Get:51 http://ftpmaster.internal/ubuntu oracular/universe amd64 unicode-data all 15.1.0-1 [8878 kB] 134s Get:52 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-fonttools amd64 4.46.0-1build2 [1436 kB] 135s Get:53 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py-serial amd64 3.10.0-1ubuntu3 [906 kB] 135s Get:54 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 135s Get:55 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-hdmedians amd64 0.14.2-5.1build1 [124 kB] 135s Get:56 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 135s Get:57 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-parso all 0.8.3-1 [67.2 kB] 135s Get:58 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 135s Get:59 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-jedi all 0.19.1+ds1-1 [693 kB] 135s Get:60 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-traitlets all 5.5.0-2 [85.0 kB] 135s Get:61 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 135s Get:62 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 135s Get:63 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pexpect all 4.9-2 [48.1 kB] 135s Get:64 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 135s Get:65 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-prompt-toolkit all 3.0.46-1 [256 kB] 135s Get:66 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pure-eval all 0.2.2-2 [11.1 kB] 135s Get:67 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-stack-data all 0.6.3-1 [22.0 kB] 135s Get:68 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 135s Get:69 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-kiwisolver amd64 1.4.5-1 [51.0 kB] 135s Get:70 http://ftpmaster.internal/ubuntu oracular/main amd64 libopenjp2-7 amd64 2.5.0-2build3 [173 kB] 135s Get:71 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-pil amd64 10.3.0-2 [457 kB] 135s Get:72 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-tk amd64 3.12.3-0ubuntu1 [102 kB] 135s Get:73 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pil.imagetk amd64 10.3.0-2 [9224 B] 135s Get:74 http://ftpmaster.internal/ubuntu oracular/main amd64 python3-packaging all 24.0-1 [41.1 kB] 135s Get:75 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-matplotlib amd64 3.6.3-2ubuntu1 [6080 kB] 135s Get:76 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-natsort all 8.0.2-2 [33.8 kB] 135s Get:77 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas-lib amd64 2.1.4+dfsg-8 [4450 kB] 135s Get:78 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 135s Get:79 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 135s Get:80 http://ftpmaster.internal/ubuntu oracular-proposed/universe amd64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 135s Get:81 http://ftpmaster.internal/ubuntu oracular/universe amd64 python3-skbio amd64 0.5.9-4build1 [750 kB] 135s Fetched 69.4 MB in 1s (130 MB/s) 135s Selecting previously unselected package libtcl8.6:amd64. 135s (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 ... 74365 files and directories currently installed.) 135s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_amd64.deb ... 135s Unpacking libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 135s Selecting previously unselected package libxrender1:amd64. 135s Preparing to unpack .../01-libxrender1_1%3a0.9.10-1.1build1_amd64.deb ... 135s Unpacking libxrender1:amd64 (1:0.9.10-1.1build1) ... 135s Selecting previously unselected package libxft2:amd64. 135s Preparing to unpack .../02-libxft2_2.3.6-1build1_amd64.deb ... 135s Unpacking libxft2:amd64 (2.3.6-1build1) ... 135s Selecting previously unselected package x11-common. 135s Preparing to unpack .../03-x11-common_1%3a7.7+23ubuntu3_all.deb ... 135s Unpacking x11-common (1:7.7+23ubuntu3) ... 135s Selecting previously unselected package libxss1:amd64. 135s Preparing to unpack .../04-libxss1_1%3a1.2.3-1build3_amd64.deb ... 135s Unpacking libxss1:amd64 (1:1.2.3-1build3) ... 135s Selecting previously unselected package libtk8.6:amd64. 135s Preparing to unpack .../05-libtk8.6_8.6.14-1build1_amd64.deb ... 135s Unpacking libtk8.6:amd64 (8.6.14-1build1) ... 136s Selecting previously unselected package tk8.6-blt2.5. 136s Preparing to unpack .../06-tk8.6-blt2.5_2.5.3+dfsg-7build1_amd64.deb ... 136s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 136s Selecting previously unselected package blt. 136s Preparing to unpack .../07-blt_2.5.3+dfsg-7build1_amd64.deb ... 136s Unpacking blt (2.5.3+dfsg-7build1) ... 136s Selecting previously unselected package fonts-lyx. 136s Preparing to unpack .../08-fonts-lyx_2.4.0-1_all.deb ... 136s Unpacking fonts-lyx (2.4.0-1) ... 136s Selecting previously unselected package libaec0:amd64. 136s Preparing to unpack .../09-libaec0_1.1.3-1_amd64.deb ... 136s Unpacking libaec0:amd64 (1.1.3-1) ... 136s Selecting previously unselected package libblas3:amd64. 136s Preparing to unpack .../10-libblas3_3.12.0-3build1_amd64.deb ... 136s Unpacking libblas3:amd64 (3.12.0-3build1) ... 136s Selecting previously unselected package libgfortran5:amd64. 136s Preparing to unpack .../11-libgfortran5_14.1.0-1ubuntu1_amd64.deb ... 136s Unpacking libgfortran5:amd64 (14.1.0-1ubuntu1) ... 136s Selecting previously unselected package libgomp1:amd64. 136s Preparing to unpack .../12-libgomp1_14.1.0-1ubuntu1_amd64.deb ... 136s Unpacking libgomp1:amd64 (14.1.0-1ubuntu1) ... 136s Selecting previously unselected package libgraphite2-3:amd64. 136s Preparing to unpack .../13-libgraphite2-3_1.3.14-2build1_amd64.deb ... 136s Unpacking libgraphite2-3:amd64 (1.3.14-2build1) ... 136s Selecting previously unselected package libharfbuzz0b:amd64. 136s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_amd64.deb ... 136s Unpacking libharfbuzz0b:amd64 (8.3.0-2build2) ... 136s Selecting previously unselected package libsz2:amd64. 136s Preparing to unpack .../15-libsz2_1.1.3-1_amd64.deb ... 136s Unpacking libsz2:amd64 (1.1.3-1) ... 136s Selecting previously unselected package libhdf5-103-1t64:amd64. 136s Preparing to unpack .../16-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 136s Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 136s Selecting previously unselected package libhdf5-hl-100t64:amd64. 136s Preparing to unpack .../17-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_amd64.deb ... 136s Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 136s Selecting previously unselected package libimagequant0:amd64. 136s Preparing to unpack .../18-libimagequant0_2.18.0-1build1_amd64.deb ... 136s Unpacking libimagequant0:amd64 (2.18.0-1build1) ... 136s Selecting previously unselected package libjs-jquery. 136s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 136s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 136s Selecting previously unselected package libjs-jquery-ui. 136s Preparing to unpack .../20-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 136s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 136s Selecting previously unselected package liblapack3:amd64. 136s Preparing to unpack .../21-liblapack3_3.12.0-3build1_amd64.deb ... 136s Unpacking liblapack3:amd64 (3.12.0-3build1) ... 136s Selecting previously unselected package liblbfgsb0:amd64. 136s Preparing to unpack .../22-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 136s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 136s Selecting previously unselected package liblcms2-2:amd64. 136s Preparing to unpack .../23-liblcms2-2_2.14-2build1_amd64.deb ... 136s Unpacking liblcms2-2:amd64 (2.14-2build1) ... 136s Selecting previously unselected package liblzf1:amd64. 136s Preparing to unpack .../24-liblzf1_3.6-4_amd64.deb ... 136s Unpacking liblzf1:amd64 (3.6-4) ... 136s Selecting previously unselected package libqhull-r8.0:amd64. 136s Preparing to unpack .../25-libqhull-r8.0_2020.2-6build1_amd64.deb ... 136s Unpacking libqhull-r8.0:amd64 (2020.2-6build1) ... 136s Selecting previously unselected package libraqm0:amd64. 136s Preparing to unpack .../26-libraqm0_0.10.1-1build1_amd64.deb ... 136s Unpacking libraqm0:amd64 (0.10.1-1build1) ... 136s Selecting previously unselected package libssw0:amd64. 136s Preparing to unpack .../27-libssw0_1.1-14build1_amd64.deb ... 136s Unpacking libssw0:amd64 (1.1-14build1) ... 136s Selecting previously unselected package libwebpdemux2:amd64. 136s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_amd64.deb ... 136s Unpacking libwebpdemux2:amd64 (1.4.0-0.1) ... 136s Selecting previously unselected package libwebpmux3:amd64. 136s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_amd64.deb ... 136s Unpacking libwebpmux3:amd64 (1.4.0-0.1) ... 136s Selecting previously unselected package libxslt1.1:amd64. 136s Preparing to unpack .../30-libxslt1.1_1.1.39-0exp1build1_amd64.deb ... 136s Unpacking libxslt1.1:amd64 (1.1.39-0exp1build1) ... 136s Selecting previously unselected package python-matplotlib-data. 136s Preparing to unpack .../31-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 136s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 136s Selecting previously unselected package python3-appdirs. 136s Preparing to unpack .../32-python3-appdirs_1.4.4-4_all.deb ... 136s Unpacking python3-appdirs (1.4.4-4) ... 136s Selecting previously unselected package python3-asttokens. 136s Preparing to unpack .../33-python3-asttokens_2.4.1-1_all.deb ... 136s Unpacking python3-asttokens (2.4.1-1) ... 136s Selecting previously unselected package python3-brotli. 136s Preparing to unpack .../34-python3-brotli_1.1.0-2build2_amd64.deb ... 136s Unpacking python3-brotli (1.1.0-2build2) ... 137s Selecting previously unselected package python3-numpy. 137s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-10_amd64.deb ... 137s Unpacking python3-numpy (1:1.26.4+ds-10) ... 137s Selecting previously unselected package python3-contourpy. 137s Preparing to unpack .../36-python3-contourpy_1.0.7-3_amd64.deb ... 137s Unpacking python3-contourpy (1.0.7-3) ... 137s Selecting previously unselected package python3-cycler. 137s Preparing to unpack .../37-python3-cycler_0.12.1-1_all.deb ... 137s Unpacking python3-cycler (0.12.1-1) ... 137s Selecting previously unselected package python3-dateutil. 137s Preparing to unpack .../38-python3-dateutil_2.9.0-2_all.deb ... 137s Unpacking python3-dateutil (2.9.0-2) ... 137s Selecting previously unselected package python3-decorator. 137s Preparing to unpack .../39-python3-decorator_5.1.1-5_all.deb ... 137s Unpacking python3-decorator (5.1.1-5) ... 137s Selecting previously unselected package python3-executing. 137s Preparing to unpack .../40-python3-executing_2.0.1-0.1_all.deb ... 137s Unpacking python3-executing (2.0.1-0.1) ... 137s Selecting previously unselected package python3-scipy. 137s Preparing to unpack .../41-python3-scipy_1.11.4-10_amd64.deb ... 137s Unpacking python3-scipy (1.11.4-10) ... 137s Selecting previously unselected package python3-ufolib2. 137s Preparing to unpack .../42-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 137s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 137s Selecting previously unselected package python3-mpmath. 137s Preparing to unpack .../43-python3-mpmath_1.3.0-1_all.deb ... 137s Unpacking python3-mpmath (1.3.0-1) ... 137s Selecting previously unselected package python3-sympy. 137s Preparing to unpack .../44-python3-sympy_1.12-8_all.deb ... 137s Unpacking python3-sympy (1.12-8) ... 138s Selecting previously unselected package python3-fs. 138s Preparing to unpack .../45-python3-fs_2.4.16-4_all.deb ... 138s Unpacking python3-fs (2.4.16-4) ... 138s Selecting previously unselected package python3-lxml:amd64. 138s Preparing to unpack .../46-python3-lxml_5.2.1-1_amd64.deb ... 138s Unpacking python3-lxml:amd64 (5.2.1-1) ... 138s Selecting previously unselected package python3-lz4. 138s Preparing to unpack .../47-python3-lz4_4.0.2+dfsg-1build4_amd64.deb ... 138s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 138s Selecting previously unselected package python3-unicodedata2. 138s Preparing to unpack .../48-python3-unicodedata2_15.1.0+ds-1build1_amd64.deb ... 138s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 138s Selecting previously unselected package unicode-data. 138s Preparing to unpack .../49-unicode-data_15.1.0-1_all.deb ... 138s Unpacking unicode-data (15.1.0-1) ... 138s Selecting previously unselected package python3-fonttools. 138s Preparing to unpack .../50-python3-fonttools_4.46.0-1build2_amd64.deb ... 138s Unpacking python3-fonttools (4.46.0-1build2) ... 138s Selecting previously unselected package python3-h5py-serial. 138s Preparing to unpack .../51-python3-h5py-serial_3.10.0-1ubuntu3_amd64.deb ... 138s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 138s Selecting previously unselected package python3-h5py. 138s Preparing to unpack .../52-python3-h5py_3.10.0-1ubuntu3_all.deb ... 138s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 138s Selecting previously unselected package python3-hdmedians. 138s Preparing to unpack .../53-python3-hdmedians_0.14.2-5.1build1_amd64.deb ... 138s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 138s Selecting previously unselected package python3-iniconfig. 138s Preparing to unpack .../54-python3-iniconfig_1.1.1-2_all.deb ... 138s Unpacking python3-iniconfig (1.1.1-2) ... 138s Selecting previously unselected package python3-parso. 138s Preparing to unpack .../55-python3-parso_0.8.3-1_all.deb ... 138s Unpacking python3-parso (0.8.3-1) ... 138s 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python3-pexpect. 139s Preparing to unpack .../61-python3-pexpect_4.9-2_all.deb ... 139s Unpacking python3-pexpect (4.9-2) ... 139s Selecting previously unselected package python3-wcwidth. 139s Preparing to unpack .../62-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 139s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 139s Selecting previously unselected package python3-prompt-toolkit. 139s Preparing to unpack .../63-python3-prompt-toolkit_3.0.46-1_all.deb ... 139s Unpacking python3-prompt-toolkit (3.0.46-1) ... 139s Selecting previously unselected package python3-pure-eval. 139s Preparing to unpack .../64-python3-pure-eval_0.2.2-2_all.deb ... 139s Unpacking python3-pure-eval (0.2.2-2) ... 139s Selecting previously unselected package python3-stack-data. 139s Preparing to unpack .../65-python3-stack-data_0.6.3-1_all.deb ... 139s Unpacking python3-stack-data (0.6.3-1) ... 139s Selecting previously unselected package python3-ipython. 139s Preparing to unpack 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140s Unpacking python3-pil.imagetk:amd64 (10.3.0-2) ... 140s Selecting previously unselected package python3-packaging. 140s Preparing to unpack .../72-python3-packaging_24.0-1_all.deb ... 140s Unpacking python3-packaging (24.0-1) ... 140s Selecting previously unselected package python3-matplotlib. 140s Preparing to unpack .../73-python3-matplotlib_3.6.3-2ubuntu1_amd64.deb ... 140s Unpacking python3-matplotlib (3.6.3-2ubuntu1) ... 140s Selecting previously unselected package python3-natsort. 140s Preparing to unpack .../74-python3-natsort_8.0.2-2_all.deb ... 140s Unpacking python3-natsort (8.0.2-2) ... 140s Selecting previously unselected package python3-pandas-lib:amd64. 140s Preparing to unpack .../75-python3-pandas-lib_2.1.4+dfsg-8_amd64.deb ... 140s Unpacking python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... 140s Selecting previously unselected package python3-pandas. 140s Preparing to unpack .../76-python3-pandas_2.1.4+dfsg-8_all.deb ... 140s Unpacking python3-pandas (2.1.4+dfsg-8) ... 140s Selecting previously unselected package python3-pluggy. 140s Preparing to unpack .../77-python3-pluggy_1.5.0-1_all.deb ... 140s Unpacking python3-pluggy (1.5.0-1) ... 140s Selecting previously unselected package python3-pytest. 140s Preparing to unpack .../78-python3-pytest_8.2.2-1ubuntu1_all.deb ... 140s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 140s Selecting previously unselected package python3-skbio. 140s Preparing to unpack .../79-python3-skbio_0.5.9-4build1_amd64.deb ... 140s Unpacking python3-skbio (0.5.9-4build1) ... 141s Selecting previously unselected package autopkgtest-satdep. 141s Preparing to unpack .../80-1-autopkgtest-satdep.deb ... 141s Unpacking autopkgtest-satdep (0) ... 141s Setting up libgraphite2-3:amd64 (1.3.14-2build1) ... 141s Setting up liblcms2-2:amd64 (2.14-2build1) ... 141s Setting up python3-iniconfig (1.1.1-2) ... 141s Setting up python3-pure-eval (0.2.2-2) ... 141s Setting up libxrender1:amd64 (1:0.9.10-1.1build1) ... 141s Setting up python3-parso (0.8.3-1) ... 141s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 141s Setting up python3-asttokens (2.4.1-1) ... 141s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 141s Setting up fonts-lyx (2.4.0-1) ... 141s Setting up libwebpdemux2:amd64 (1.4.0-0.1) ... 141s Setting up x11-common (1:7.7+23ubuntu3) ... 142s Setting up libqhull-r8.0:amd64 (2020.2-6build1) ... 142s Setting up libgomp1:amd64 (14.1.0-1ubuntu1) ... 142s Setting up libaec0:amd64 (1.1.3-1) ... 142s Setting up python3-natsort (8.0.2-2) ... 142s Setting up unicode-data (15.1.0-1) ... 142s Setting up python3-decorator (5.1.1-5) ... 142s Setting up libblas3:amd64 (3.12.0-3build1) ... 142s 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 142s Setting up python3-packaging (24.0-1) ... 142s Setting up python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 142s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 142s Setting up python3-executing (2.0.1-0.1) ... 142s Setting up python3-brotli (1.1.0-2build2) ... 143s Setting up liblzf1:amd64 (3.6-4) ... 143s Setting up python3-cycler (0.12.1-1) ... 143s Setting up libimagequant0:amd64 (2.18.0-1build1) ... 143s Setting up python3-kiwisolver (1.4.5-1) ... 143s Setting up libtcl8.6:amd64 (8.6.14+dfsg-1build1) ... 143s Setting up libgfortran5:amd64 (14.1.0-1ubuntu1) ... 143s Setting up python3-pluggy (1.5.0-1) ... 143s Setting up python3-traitlets (5.5.0-2) ... 143s Setting up libxslt1.1:amd64 (1.1.39-0exp1build1) ... 143s Setting up libopenjp2-7:amd64 (2.5.0-2build3) ... 143s Setting up libharfbuzz0b:amd64 (8.3.0-2build2) ... 143s Setting up python3-dateutil (2.9.0-2) ... 143s Setting up libxss1:amd64 (1:1.2.3-1build3) ... 143s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 143s Setting up python3-mpmath (1.3.0-1) ... 144s Setting up python-matplotlib-data (3.6.3-2ubuntu1) ... 144s Setting up libwebpmux3:amd64 (1.4.0-0.1) ... 144s Setting up python3-appdirs (1.4.4-4) ... 144s Setting up python3-stack-data (0.6.3-1) ... 144s Setting up libssw0:amd64 (1.1-14build1) ... 144s Setting up libsz2:amd64 (1.1.3-1) ... 144s Setting up python3-ptyprocess (0.7.0-5) ... 144s Setting up python3-prompt-toolkit (3.0.46-1) ... 145s Setting up python3-sympy (1.12-8) ... 151s Setting up liblapack3:amd64 (3.12.0-3build1) ... 151s 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 151s Setting up libxft2:amd64 (2.3.6-1build1) ... 151s Setting up python3-jedi (0.19.1+ds1-1) ... 151s Setting up python3-pytest (8.2.2-1ubuntu1) ... 151s Setting up libtk8.6:amd64 (8.6.14-1build1) ... 151s Setting up python3-matplotlib-inline (0.1.6-2) ... 151s Setting up python3-fs (2.4.16-4) ... 152s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 152s Setting up python3-pexpect (4.9-2) ... 152s Setting up libraqm0:amd64 (0.10.1-1build1) ... 152s Setting up python3-numpy (1:1.26.4+ds-10) ... 154s Setting up python3-hdmedians (0.14.2-5.1build1) ... 154s Setting up python3-lxml:amd64 (5.2.1-1) ... 154s Setting up python3-contourpy (1.0.7-3) ... 154s Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 154s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 154s Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.1ubuntu4) ... 154s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 154s Setting up python3-scipy (1.11.4-10) ... 157s Setting up blt (2.5.3+dfsg-7build1) ... 157s Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-8) ... 157s Setting up python3-h5py-serial (3.10.0-1ubuntu3) ... 157s Setting up python3-tk:amd64 (3.12.3-0ubuntu1) ... 158s Setting up python3-pil:amd64 (10.3.0-2) ... 158s Setting up python3-pandas (2.1.4+dfsg-8) ... 162s Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... 163s Setting up python3-ipython (8.20.0-1ubuntu1) ... 163s Setting up python3-h5py (3.10.0-1ubuntu3) ... 163s Setting up python3-fonttools (4.46.0-1build2) ... 164s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 164s Setting up python3-matplotlib (3.6.3-2ubuntu1) ... 166s Setting up python3-skbio (0.5.9-4build1) ... 166s Setting up autopkgtest-satdep (0) ... 166s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 166s Processing triggers for man-db (2.12.1-1) ... 170s (Reading database ... 91253 files and directories currently installed.) 170s Removing autopkgtest-satdep (0) ... 171s autopkgtest [00:28:00]: test import-skbio: [----------------------- 173s autopkgtest [00:28:02]: test import-skbio: -----------------------] 173s autopkgtest [00:28:02]: test import-skbio: - - - - - - - - - - results - - - - - - - - - - 173s import-skbio PASS 173s autopkgtest [00:28:02]: test testsuite: preparing testbed 173s Reading package lists... 174s Building dependency tree... 174s Reading state information... 174s Starting pkgProblemResolver with broken count: 0 174s Starting 2 pkgProblemResolver with broken count: 0 174s Done 175s The following NEW packages will be installed: 175s autopkgtest-satdep 175s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 175s Need to get 0 B/716 B of archives. 175s After this operation, 0 B of additional disk space will be used. 175s Get:1 /tmp/autopkgtest.hddjcZ/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 175s Selecting previously unselected package autopkgtest-satdep. 175s (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 ... 91253 files and directories currently installed.) 175s Preparing to unpack .../2-autopkgtest-satdep.deb ... 175s Unpacking autopkgtest-satdep (0) ... 175s Setting up autopkgtest-satdep (0) ... 177s (Reading database ... 91253 files and directories currently installed.) 177s Removing autopkgtest-satdep (0) ... 177s autopkgtest [00:28:06]: test testsuite: [----------------------- 177s + 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 {} ; 177s + 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 {} ; 177s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 180s ============================= test session starts ============================== 180s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 180s rootdir: /tmp/autopkgtest.hddjcZ/autopkgtest_tmp 180s collected 2390 items 180s 180s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 180s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 180s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 181s ........................................................................ 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[ 33%] 201s skbio/io/format/tests/test_phylip.py ....... [ 33%] 202s skbio/io/format/tests/test_qseq.py ...... [ 33%] 202s skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 34%] 203s skbio/io/format/tests/test_stockholm.py ................................ [ 35%] 203s ........................................... [ 37%] 203s skbio/io/format/tests/test_taxdump.py ...... [ 37%] 203s skbio/io/tests/test_iosources.py .......... [ 37%] 203s skbio/io/tests/test_registry.py ........................................ [ 39%] 203s ...................................................... [ 41%] 205s skbio/io/tests/test_util.py .......................................XXsss [ 43%] 207s sssssssssssssssssssssssssss..................................xx......... [ 46%] 210s .........................xx..................................xx......... [ 49%] 211s .........................xx..... [ 51%] 212s skbio/metadata/tests/test_intersection.py ............... 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[ 66%] 213s ........................................................................ [ 69%] 213s ........................................................................ [ 72%] 213s ........................................................................ [ 75%] 213s ....... [ 75%] 214s skbio/stats/distance/tests/test_anosim.py .... [ 75%] 214s skbio/stats/distance/tests/test_base.py ................................ [ 76%] 214s ................................................................... [ 79%] 220s skbio/stats/distance/tests/test_bioenv.py ................. [ 80%] 222s skbio/stats/distance/tests/test_mantel.py .............................. [ 81%] 223s .............. [ 82%] 223s skbio/stats/distance/tests/test_permanova.py .... [ 82%] 227s skbio/stats/distance/tests/test_permdisp.py ............. [ 82%] 227s skbio/stats/evolve/tests/test_hommola.py ............ [ 83%] 227s skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%] 227s ..... [ 83%] 228s skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 84%] 228s skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%] 228s [ 84%] 228s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 84%] 228s ....... [ 85%] 229s skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 85%] 229s skbio/stats/ordination/tests/test_util.py .......... [ 85%] 229s skbio/stats/tests/test_composition.py .................................. [ 87%] 229s ............................... [ 88%] 229s skbio/stats/tests/test_gradient.py .......................... [ 89%] 229s skbio/stats/tests/test_misc.py ... [ 89%] 231s skbio/stats/tests/test_power.py ........................................ [ 91%] 232s ... [ 91%] 232s skbio/stats/tests/test_subsample.py ............ [ 92%] 232s skbio/tests/test_base.py ..... [ 92%] 232s skbio/tests/test_workflow.py ................. [ 92%] 232s skbio/tree/tests/test_majority_rule.py ...... [ 93%] 232s skbio/tree/tests/test_nj.py ........... [ 93%] 232s skbio/tree/tests/test_tree.py .......................................... [ 95%] 232s ................................................... [ 97%] 232s skbio/util/tests/test_decorator.py ....................... [ 98%] 232s skbio/util/tests/test_misc.py .................... [ 99%] 232s skbio/util/tests/test_testing.py ............... [100%] 232s 232s =============================== warnings summary =============================== 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 232s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: local_pairwise_align_ssw is deprecated as of scikit-bio version 0.5.8, and will be removed in version 0.6.0. This will be removed or replaced, in favor of more general-purpose performant aligners. Additional details at https://github.com/biocore/scikit-bio/issues/1814 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 232s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 232s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/metadata/_testing.py:445: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 232s df['bar'][0].append(42) 232s 232s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 232s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 232s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/metadata/_testing.py:823: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 232s df['bar'][0].append(42) 232s 232s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 232s gap_freqs /= length 232s 232s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 232s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 232s 232s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 232s freqs = counts / counts.sum() 232s 232s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 232s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 232s 232s skbio/diversity/tests/test_block.py: 3 warnings 232s skbio/diversity/tests/test_driver.py: 9 warnings 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. 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. 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 232s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 232s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: nondegenerates is deprecated as of scikit-bio version 0.5.0, and will be removed in version 0.6.0. Renamed to definites 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 232s obs_counts = obs_counts / len(self) 232s 232s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 232s warnings.warn(ConstantInputWarning()) 232s 232s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 232s warnings.warn(ConstantInputWarning()) 232s 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: 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. 232s warn( 232s 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: 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. 232s warn( 232s 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 232s proportion_explained = eigvals / sum_eigenvalues 232s 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 232s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 232s /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4167: ConstantInputWarning: Each of the input arrays is constant;the F statistic is not defined or infinite 232s warnings.warn(stats.ConstantInputWarning(msg)) 232s 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 232s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:143: 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. 232s warn( 232s 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:285: UserWarning: Tight layout not applied. The left and right margins cannot be made large enough to accommodate all axes decorations. 232s fig.tight_layout() 232s 232s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 232s plot = scatter_fn(c=point_colors, cmap=cmap) 232s 232s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 232s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 232s return self.run(*args, **kwds) 232s 232s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/ordination/tests/test_redundancy_analysis.py:248: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 232s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 232s 232s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 232s /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:523: RuntimeWarning: Precision loss occurred in moment calculation due to catastrophic cancellation. This occurs when the data are nearly identical. Results may be unreliable. 232s res = hypotest_fun_out(*samples, **kwds) 232s 232s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 232s X_log = np.log(mat) 232s 232s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 232s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 232s X -= avg[:, None] 232s 232s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 232s x = np.log(x) 232s 232s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 232s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 232s x = asanyarray(arr - arrmean) 232s 232s skbio/stats/tests/test_gradient.py: 13 warnings 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/gradient.py:168: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]` 232s np.abs((w_vector[i] - w_vector[i-1])) 232s 232s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/gradient.py:166: FutureWarning: Setting an item of incompatible dtype is deprecated and will raise in a future error of pandas. Value '6.357142857142857' has dtype incompatible with int64, please explicitly cast to a compatible dtype first. 232s trajectories.loc[idx] = ( 232s 232s skbio/stats/tests/test_power.py: 27 warnings 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/stats/power.py:1122: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 232s pwr[id2] = _calculate_power(ps, a) 232s 232s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 232s /tmp/autopkgtest.hddjcZ/autopkgtest_tmp/skbio/util/_decorator.py:254: DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will be removed in version 0.1.4. You should now use skbio.g(). 232s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 232s 232s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 232s ==== 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 119 warnings in 55.04s ===== 233s autopkgtest [00:29:02]: test testsuite: -----------------------] 233s testsuite PASS 233s autopkgtest [00:29:02]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 234s autopkgtest [00:29:03]: @@@@@@@@@@@@@@@@@@@@ summary 234s import-skbio PASS 234s testsuite PASS 244s nova [W] Skipping flock for amd64 244s Creating nova instance adt-oracular-amd64-python-skbio-20240608-002508-juju-7f2275-prod-proposed-migration-environment-2-7a84b354-8785-4b66-8c16-de5e7bf2996d from image adt/ubuntu-oracular-amd64-server-20240607.img (UUID d996b44c-1e10-4875-aeab-5b4c434d75a2)...