0s autopkgtest [03:17:08]: starting date and time: 2024-03-24 03:17:08+0000 0s autopkgtest [03:17:08]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:17:08]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9fpjetgh/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:sphinx --apt-upgrade python-skbio --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=sphinx/7.2.6-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-arm64-2.secgroup --name adt-noble-arm64-python-skbio-20240324-031708-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 99s autopkgtest [03:18:47]: testbed dpkg architecture: arm64 99s autopkgtest [03:18:47]: testbed apt version: 2.7.12 99s autopkgtest [03:18:47]: @@@@@@@@@@@@@@@@@@@@ test bed setup 100s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 101s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 101s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 101s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 101s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 101s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [707 kB] 101s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 101s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 101s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 101s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4363 kB] 102s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 102s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [69.8 kB] 102s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 107s Fetched 9845 kB in 3s (3362 kB/s) 108s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s sh: Attempting to set up Debian/Ubuntu apt sources automatically 117s sh: Distribution appears to be Ubuntu 119s Reading package lists... 120s Building dependency tree... 120s Reading state information... 121s eatmydata is already the newest version (131-1). 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 123s dbus is already the newest version (1.14.10-4ubuntu1). 123s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 123s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s rng-tools-debian is already the newest version (2.4). 124s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s The following packages will be REMOVED: 126s cloud-init* python3-configobj* python3-debconf* 127s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 127s After this operation, 3256 kB disk space will be freed. 127s (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 ... 75911 files and directories currently installed.) 127s Removing cloud-init (24.1.2-0ubuntu1) ... 128s Removing python3-configobj (5.0.8-3) ... 128s Removing python3-debconf (1.5.86) ... 129s Processing triggers for man-db (2.12.0-3) ... 129s (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 ... 75522 files and directories currently installed.) 129s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 131s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 131s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 131s invoke-rc.d: policy-rc.d denied execution of try-restart. 131s Reading package lists... 132s Building dependency tree... 132s Reading state information... 133s linux-generic is already the newest version (6.8.0-11.11+1). 133s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 133s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 134s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 134s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 139s Reading package lists... 139s Reading package lists... 140s Building dependency tree... 140s Reading state information... 141s Calculating upgrade... 142s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s Reading package lists... 142s Building dependency tree... 142s Reading state information... 143s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 144s autopkgtest [03:19:32]: rebooting testbed after setup commands that affected boot 299s autopkgtest [03:22:06]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 302s autopkgtest [03:22:10]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 305s Get:1 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (dsc) [2804 B] 305s Get:2 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (tar) [3559 kB] 305s Get:3 http://ftpmaster.internal/ubuntu noble/universe python-skbio 0.5.9-4 (diff) [15.7 kB] 306s gpgv: Signature made Sun Feb 11 20:35:02 2024 UTC 306s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 306s gpgv: issuer "tille@debian.org" 306s gpgv: Can't check signature: No public key 306s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4.dsc: no acceptable signature found 306s autopkgtest [03:22:14]: testing package python-skbio version 0.5.9-4 306s autopkgtest [03:22:14]: build not needed 307s autopkgtest [03:22:15]: test import-skbio: preparing testbed 310s Reading package lists... 311s Building dependency tree... 311s Reading state information... 311s Starting pkgProblemResolver with broken count: 0 311s Starting 2 pkgProblemResolver with broken count: 0 311s Done 313s The following additional packages will be installed: 313s blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-lyx libaec0 313s libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 libgraphite2-3 313s libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libimagequant0 libjbig0 313s libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 313s liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libsharpyuv0 313s libssw0 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 313s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 313s python3-appdirs python3-asttokens python3-brotli python3-contourpy 313s python3-cycler python3-dateutil python3-decorator python3-executing 313s python3-fonttools python3-fs python3-h5py python3-h5py-serial 313s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 313s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 313s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 313s python3-packaging python3-pandas python3-pandas-lib python3-parso 313s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 313s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 313s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 313s python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth 313s tk8.6-blt2.5 unicode-data x11-common 313s Suggested packages: 313s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 313s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 313s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 313s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 313s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 313s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 313s gfortran python3-dev python-pandas-doc python3-statsmodels 313s python-pexpect-doc python-pil-doc python-scipy-doc python-skbio-doc 313s texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 313s Recommended packages: 313s javascript-common python3-bs4 python3-cssselect python3-html5lib 313s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 313s python3-tables python3-olefile g++ | c++-compiler isympy-common 313s The following NEW packages will be installed: 313s autopkgtest-satdep blt fontconfig-config fonts-dejavu-core fonts-dejavu-mono 313s fonts-lyx libaec0 libblas3 libdeflate0 libfontconfig1 libgfortran5 libgomp1 313s libgraphite2-3 libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libimagequant0 313s libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui liblapack3 313s liblbfgsb0 liblcms2-2 liblerc4 liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 313s libsharpyuv0 libssw0 libsz2 libtcl8.6 libtiff6 libtk8.6 libwebp7 313s libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 313s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 313s python3-contourpy python3-cycler python3-dateutil python3-decorator 313s python3-executing python3-fonttools python3-fs python3-h5py 313s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 313s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 313s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 313s python3-packaging python3-pandas python3-pandas-lib python3-parso 313s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 313s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 313s python3-scipy python3-skbio python3-stack-data python3-sympy python3-tk 313s python3-traitlets python3-ufolib2 python3-unicodedata2 python3-wcwidth 313s tk8.6-blt2.5 unicode-data x11-common 313s 0 upgraded, 92 newly installed, 0 to remove and 0 not upgraded. 313s Need to get 78.8 MB/78.8 MB of archives. 313s After this operation, 385 MB of additional disk space will be used. 313s Get:1 /tmp/autopkgtest.QcvHYo/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 313s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [980 kB] 313s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-mono all 2.37-8 [502 kB] 313s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 fonts-dejavu-core all 2.37-8 [835 kB] 313s Get:5 http://ftpmaster.internal/ubuntu noble/main arm64 fontconfig-config arm64 2.15.0-1ubuntu1 [37.0 kB] 313s Get:6 http://ftpmaster.internal/ubuntu noble/main arm64 libfontconfig1 arm64 2.15.0-1ubuntu1 [142 kB] 313s Get:7 http://ftpmaster.internal/ubuntu noble/main arm64 libxrender1 arm64 1:0.9.10-1.1 [19.1 kB] 313s Get:8 http://ftpmaster.internal/ubuntu noble/main arm64 libxft2 arm64 2.3.6-1 [43.3 kB] 313s Get:9 http://ftpmaster.internal/ubuntu noble/main arm64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 313s Get:10 http://ftpmaster.internal/ubuntu noble/main arm64 libxss1 arm64 1:1.2.3-1build2 [8252 B] 313s Get:11 http://ftpmaster.internal/ubuntu noble/main arm64 libtk8.6 arm64 8.6.14-1 [767 kB] 313s Get:12 http://ftpmaster.internal/ubuntu noble/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7 [618 kB] 313s Get:13 http://ftpmaster.internal/ubuntu noble/main arm64 blt arm64 2.5.3+dfsg-7 [4826 B] 314s Get:14 http://ftpmaster.internal/ubuntu noble/universe arm64 fonts-lyx all 2.4.0~RC3-1 [170 kB] 314s Get:15 http://ftpmaster.internal/ubuntu noble/universe arm64 libaec0 arm64 1.1.2-1 [21.7 kB] 314s Get:16 http://ftpmaster.internal/ubuntu noble/main arm64 libblas3 arm64 3.12.0-3 [143 kB] 314s Get:17 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 314s Get:18 http://ftpmaster.internal/ubuntu noble/main arm64 libgfortran5 arm64 14-20240303-1ubuntu1 [444 kB] 314s Get:19 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 314s Get:20 http://ftpmaster.internal/ubuntu noble/main arm64 libgraphite2-3 arm64 1.3.14-2 [81.5 kB] 314s Get:21 http://ftpmaster.internal/ubuntu noble/main arm64 libharfbuzz0b arm64 8.3.0-2 [463 kB] 314s Get:22 http://ftpmaster.internal/ubuntu noble/universe arm64 libsz2 arm64 1.1.2-1 [5168 B] 314s Get:23 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-103-1 arm64 1.10.10+repack-3ubuntu1 [1189 kB] 314s Get:24 http://ftpmaster.internal/ubuntu noble/universe arm64 libhdf5-hl-100 arm64 1.10.10+repack-3ubuntu1 [55.5 kB] 314s Get:25 http://ftpmaster.internal/ubuntu noble/main arm64 libimagequant0 arm64 2.18.0-1 [37.0 kB] 314s Get:26 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg-turbo8 arm64 2.1.5-2ubuntu1 [160 kB] 314s Get:27 http://ftpmaster.internal/ubuntu noble/main arm64 libjpeg8 arm64 8c-2ubuntu11 [2148 B] 314s Get:28 http://ftpmaster.internal/ubuntu noble/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 314s Get:29 http://ftpmaster.internal/ubuntu noble/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 314s Get:30 http://ftpmaster.internal/ubuntu noble/main arm64 liblapack3 arm64 3.12.0-3 [2241 kB] 314s Get:31 http://ftpmaster.internal/ubuntu noble/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [27.7 kB] 314s Get:32 http://ftpmaster.internal/ubuntu noble/main arm64 liblcms2-2 arm64 2.14-2 [159 kB] 314s Get:33 http://ftpmaster.internal/ubuntu noble/main arm64 liblerc4 arm64 4.0.0+ds-4ubuntu1 [153 kB] 314s Get:34 http://ftpmaster.internal/ubuntu noble/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 314s Get:35 http://ftpmaster.internal/ubuntu noble/universe arm64 libqhull-r8.0 arm64 2020.2-6 [188 kB] 314s Get:36 http://ftpmaster.internal/ubuntu noble/main arm64 libraqm0 arm64 0.10.1-1 [14.4 kB] 314s Get:37 http://ftpmaster.internal/ubuntu noble/main arm64 libsharpyuv0 arm64 1.3.2-0.4 [14.4 kB] 314s Get:38 http://ftpmaster.internal/ubuntu noble/universe arm64 libssw0 arm64 1.1-14 [21.1 kB] 314s Get:39 http://ftpmaster.internal/ubuntu noble/main arm64 libjbig0 arm64 2.1-6.1ubuntu1 [28.9 kB] 314s Get:40 http://ftpmaster.internal/ubuntu noble/main arm64 libwebp7 arm64 1.3.2-0.4 [191 kB] 314s Get:41 http://ftpmaster.internal/ubuntu noble/main arm64 libtiff6 arm64 4.5.1+git230720-3ubuntu1 [226 kB] 314s Get:42 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpdemux2 arm64 1.3.2-0.4 [12.3 kB] 314s Get:43 http://ftpmaster.internal/ubuntu noble/main arm64 libwebpmux3 arm64 1.3.2-0.4 [25.0 kB] 314s Get:44 http://ftpmaster.internal/ubuntu noble/main arm64 libxslt1.1 arm64 1.1.39-0exp1 [166 kB] 314s Get:45 http://ftpmaster.internal/ubuntu noble/universe arm64 python-matplotlib-data all 3.6.3-1ubuntu3 [2936 kB] 314s Get:46 http://ftpmaster.internal/ubuntu noble/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 314s Get:47 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-asttokens all 2.4.1-1 [20.9 kB] 314s Get:48 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-brotli arm64 1.1.0-2 [345 kB] 314s Get:49 http://ftpmaster.internal/ubuntu noble/main arm64 python3-numpy arm64 1:1.24.2-2 [4525 kB] 314s Get:50 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-contourpy arm64 1.0.7-1build2 [244 kB] 314s Get:51 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-cycler all 0.11.0-2 [8202 B] 314s Get:52 http://ftpmaster.internal/ubuntu noble/main arm64 python3-dateutil all 2.8.2-3 [79.2 kB] 314s Get:53 http://ftpmaster.internal/ubuntu noble/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 314s Get:54 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-executing all 2.0.1-0.1 [23.3 kB] 314s Get:55 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-scipy arm64 1.11.4-6 [18.6 MB] 315s Get:56 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 315s Get:57 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-mpmath all 1.2.1-3 [421 kB] 315s Get:58 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-sympy all 1.12-7 [3966 kB] 315s Get:59 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fs all 2.4.16-3 [91.1 kB] 315s Get:60 http://ftpmaster.internal/ubuntu noble/main arm64 python3-lxml arm64 5.1.0-1 [2042 kB] 315s Get:61 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build2 [28.4 kB] 315s Get:62 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1 [362 kB] 315s Get:63 http://ftpmaster.internal/ubuntu noble/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 315s Get:64 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-fonttools arm64 4.46.0-1 [1625 kB] 315s Get:65 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu1 [1462 kB] 315s Get:66 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-h5py all 3.10.0-1ubuntu1 [7970 B] 315s Get:67 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-hdmedians arm64 0.14.2-5.1 [170 kB] 315s Get:68 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 315s Get:69 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 315s Get:70 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-jedi all 0.18.2-1ubuntu1 [692 kB] 315s Get:71 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 315s Get:72 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 315s Get:73 http://ftpmaster.internal/ubuntu noble/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 315s Get:74 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 315s Get:75 http://ftpmaster.internal/ubuntu noble/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 315s Get:76 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-prompt-toolkit all 3.0.43-1 [256 kB] 315s Get:77 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pure-eval all 0.2.2-1 [11.3 kB] 315s Get:78 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 315s Get:79 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-ipython all 8.20.0-1 [561 kB] 315s Get:80 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-kiwisolver arm64 1.4.4-2 [48.5 kB] 315s Get:81 http://ftpmaster.internal/ubuntu noble/main arm64 libopenjp2-7 arm64 2.5.0-2 [170 kB] 315s Get:82 http://ftpmaster.internal/ubuntu noble/main arm64 python3-pil arm64 10.2.0-1 [477 kB] 315s Get:83 http://ftpmaster.internal/ubuntu noble/main arm64 python3-tk arm64 3.11.5-1 [112 kB] 315s Get:84 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pil.imagetk arm64 10.2.0-1 [9708 B] 315s Get:85 http://ftpmaster.internal/ubuntu noble/main arm64 python3-packaging all 23.2-1 [40.6 kB] 315s Get:86 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-matplotlib arm64 3.6.3-1ubuntu3 [7291 kB] 315s Get:87 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 315s Get:88 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-4ubuntu2 [7669 kB] 315s Get:89 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pandas all 2.1.4+dfsg-4ubuntu2 [3042 kB] 316s Get:90 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pluggy all 1.4.0-1 [20.4 kB] 316s Get:91 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-pytest all 7.4.4-1 [305 kB] 316s Get:92 http://ftpmaster.internal/ubuntu noble/universe arm64 python3-skbio arm64 0.5.9-4 [883 kB] 317s Fetched 78.8 MB in 3s (27.1 MB/s) 317s Selecting previously unselected package libtcl8.6:arm64. 317s (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 ... 75467 files and directories currently installed.) 317s Preparing to unpack .../00-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... 317s Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... 317s Selecting previously unselected package fonts-dejavu-mono. 317s Preparing to unpack .../01-fonts-dejavu-mono_2.37-8_all.deb ... 317s Unpacking fonts-dejavu-mono (2.37-8) ... 317s Selecting previously unselected package fonts-dejavu-core. 317s Preparing to unpack .../02-fonts-dejavu-core_2.37-8_all.deb ... 317s Unpacking fonts-dejavu-core (2.37-8) ... 317s Selecting previously unselected package fontconfig-config. 317s Preparing to unpack .../03-fontconfig-config_2.15.0-1ubuntu1_arm64.deb ... 317s Unpacking fontconfig-config (2.15.0-1ubuntu1) ... 317s Selecting previously unselected package libfontconfig1:arm64. 317s Preparing to unpack .../04-libfontconfig1_2.15.0-1ubuntu1_arm64.deb ... 317s Unpacking libfontconfig1:arm64 (2.15.0-1ubuntu1) ... 318s Selecting previously unselected package libxrender1:arm64. 318s Preparing to unpack .../05-libxrender1_1%3a0.9.10-1.1_arm64.deb ... 318s Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... 318s Selecting previously unselected package libxft2:arm64. 318s Preparing to unpack .../06-libxft2_2.3.6-1_arm64.deb ... 318s Unpacking libxft2:arm64 (2.3.6-1) ... 318s Selecting previously unselected package x11-common. 318s Preparing to unpack .../07-x11-common_1%3a7.7+23ubuntu2_all.deb ... 318s Unpacking x11-common (1:7.7+23ubuntu2) ... 318s Selecting previously unselected package libxss1:arm64. 318s Preparing to unpack .../08-libxss1_1%3a1.2.3-1build2_arm64.deb ... 318s Unpacking libxss1:arm64 (1:1.2.3-1build2) ... 318s Selecting previously unselected package libtk8.6:arm64. 318s Preparing to unpack .../09-libtk8.6_8.6.14-1_arm64.deb ... 318s Unpacking libtk8.6:arm64 (8.6.14-1) ... 318s Selecting previously unselected package tk8.6-blt2.5. 318s Preparing to unpack .../10-tk8.6-blt2.5_2.5.3+dfsg-7_arm64.deb ... 318s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7) ... 318s Selecting previously unselected package blt. 318s Preparing to unpack .../11-blt_2.5.3+dfsg-7_arm64.deb ... 318s Unpacking blt (2.5.3+dfsg-7) ... 318s Selecting previously unselected package fonts-lyx. 318s Preparing to unpack .../12-fonts-lyx_2.4.0~RC3-1_all.deb ... 318s Unpacking fonts-lyx (2.4.0~RC3-1) ... 318s Selecting previously unselected package libaec0:arm64. 318s Preparing to unpack .../13-libaec0_1.1.2-1_arm64.deb ... 318s Unpacking libaec0:arm64 (1.1.2-1) ... 318s Selecting previously unselected package libblas3:arm64. 318s Preparing to unpack .../14-libblas3_3.12.0-3_arm64.deb ... 318s Unpacking libblas3:arm64 (3.12.0-3) ... 318s Selecting previously unselected package libdeflate0:arm64. 318s Preparing to unpack .../15-libdeflate0_1.19-1_arm64.deb ... 318s Unpacking libdeflate0:arm64 (1.19-1) ... 318s Selecting previously unselected package libgfortran5:arm64. 318s Preparing to unpack .../16-libgfortran5_14-20240303-1ubuntu1_arm64.deb ... 318s Unpacking libgfortran5:arm64 (14-20240303-1ubuntu1) ... 318s Selecting previously unselected package libgomp1:arm64. 318s Preparing to unpack .../17-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 318s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 318s Selecting previously unselected package libgraphite2-3:arm64. 318s Preparing to unpack .../18-libgraphite2-3_1.3.14-2_arm64.deb ... 318s Unpacking libgraphite2-3:arm64 (1.3.14-2) ... 318s Selecting previously unselected package libharfbuzz0b:arm64. 318s Preparing to unpack .../19-libharfbuzz0b_8.3.0-2_arm64.deb ... 318s Unpacking libharfbuzz0b:arm64 (8.3.0-2) ... 318s Selecting previously unselected package libsz2:arm64. 318s Preparing to unpack .../20-libsz2_1.1.2-1_arm64.deb ... 318s Unpacking libsz2:arm64 (1.1.2-1) ... 318s Selecting previously unselected package libhdf5-103-1:arm64. 318s Preparing to unpack .../21-libhdf5-103-1_1.10.10+repack-3ubuntu1_arm64.deb ... 318s Unpacking libhdf5-103-1:arm64 (1.10.10+repack-3ubuntu1) ... 319s Selecting previously unselected package libhdf5-hl-100:arm64. 319s Preparing to unpack .../22-libhdf5-hl-100_1.10.10+repack-3ubuntu1_arm64.deb ... 319s Unpacking libhdf5-hl-100:arm64 (1.10.10+repack-3ubuntu1) ... 319s Selecting previously unselected package libimagequant0:arm64. 319s Preparing to unpack .../23-libimagequant0_2.18.0-1_arm64.deb ... 319s Unpacking libimagequant0:arm64 (2.18.0-1) ... 319s Selecting previously unselected package libjpeg-turbo8:arm64. 319s Preparing to unpack .../24-libjpeg-turbo8_2.1.5-2ubuntu1_arm64.deb ... 319s Unpacking libjpeg-turbo8:arm64 (2.1.5-2ubuntu1) ... 319s Selecting previously unselected package libjpeg8:arm64. 319s Preparing to unpack .../25-libjpeg8_8c-2ubuntu11_arm64.deb ... 319s Unpacking libjpeg8:arm64 (8c-2ubuntu11) ... 319s Selecting previously unselected package libjs-jquery. 319s Preparing to unpack .../26-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 319s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 319s Selecting previously unselected package libjs-jquery-ui. 319s Preparing to unpack .../27-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 319s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 319s Selecting previously unselected package liblapack3:arm64. 319s Preparing to unpack .../28-liblapack3_3.12.0-3_arm64.deb ... 319s Unpacking liblapack3:arm64 (3.12.0-3) ... 319s Selecting previously unselected package liblbfgsb0:arm64. 319s Preparing to unpack .../29-liblbfgsb0_3.0+dfsg.4-1_arm64.deb ... 319s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1) ... 319s Selecting previously unselected package liblcms2-2:arm64. 319s Preparing to unpack .../30-liblcms2-2_2.14-2_arm64.deb ... 319s Unpacking liblcms2-2:arm64 (2.14-2) ... 319s Selecting previously unselected package liblerc4:arm64. 319s Preparing to unpack .../31-liblerc4_4.0.0+ds-4ubuntu1_arm64.deb ... 319s Unpacking liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 319s Selecting previously unselected package liblzf1:arm64. 319s Preparing to unpack .../32-liblzf1_3.6-4_arm64.deb ... 319s Unpacking liblzf1:arm64 (3.6-4) ... 319s Selecting previously unselected package libqhull-r8.0:arm64. 319s Preparing to unpack .../33-libqhull-r8.0_2020.2-6_arm64.deb ... 319s Unpacking libqhull-r8.0:arm64 (2020.2-6) ... 319s Selecting previously unselected package libraqm0:arm64. 319s Preparing to unpack .../34-libraqm0_0.10.1-1_arm64.deb ... 319s Unpacking libraqm0:arm64 (0.10.1-1) ... 319s Selecting previously unselected package libsharpyuv0:arm64. 319s Preparing to unpack .../35-libsharpyuv0_1.3.2-0.4_arm64.deb ... 319s Unpacking libsharpyuv0:arm64 (1.3.2-0.4) ... 319s Selecting previously unselected package libssw0:arm64. 319s Preparing to unpack .../36-libssw0_1.1-14_arm64.deb ... 319s Unpacking libssw0:arm64 (1.1-14) ... 319s Selecting previously unselected package libjbig0:arm64. 319s Preparing to unpack .../37-libjbig0_2.1-6.1ubuntu1_arm64.deb ... 319s Unpacking libjbig0:arm64 (2.1-6.1ubuntu1) ... 319s Selecting previously unselected package libwebp7:arm64. 320s Preparing to unpack .../38-libwebp7_1.3.2-0.4_arm64.deb ... 320s Unpacking libwebp7:arm64 (1.3.2-0.4) ... 320s Selecting previously unselected package libtiff6:arm64. 320s Preparing to unpack .../39-libtiff6_4.5.1+git230720-3ubuntu1_arm64.deb ... 320s Unpacking libtiff6:arm64 (4.5.1+git230720-3ubuntu1) ... 320s Selecting previously unselected package libwebpdemux2:arm64. 320s Preparing to unpack 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python3-asttokens (2.4.1-1) ... 320s Selecting previously unselected package python3-brotli. 320s Preparing to unpack .../46-python3-brotli_1.1.0-2_arm64.deb ... 320s Unpacking python3-brotli (1.1.0-2) ... 320s Selecting previously unselected package python3-numpy. 320s Preparing to unpack .../47-python3-numpy_1%3a1.24.2-2_arm64.deb ... 320s Unpacking python3-numpy (1:1.24.2-2) ... 321s Selecting previously unselected package python3-contourpy. 321s Preparing to unpack .../48-python3-contourpy_1.0.7-1build2_arm64.deb ... 321s Unpacking python3-contourpy (1.0.7-1build2) ... 321s Selecting previously unselected package python3-cycler. 321s Preparing to unpack .../49-python3-cycler_0.11.0-2_all.deb ... 321s Unpacking python3-cycler (0.11.0-2) ... 321s Selecting previously unselected package python3-dateutil. 321s Preparing to unpack .../50-python3-dateutil_2.8.2-3_all.deb ... 321s Unpacking python3-dateutil (2.8.2-3) ... 321s Selecting previously unselected package python3-decorator. 321s 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python3-parso (0.8.3-1) ... 325s Selecting previously unselected package python3-jedi. 325s Preparing to unpack .../68-python3-jedi_0.18.2-1ubuntu1_all.deb ... 325s Unpacking python3-jedi (0.18.2-1ubuntu1) ... 325s Selecting previously unselected package python3-traitlets. 325s Preparing to unpack .../69-python3-traitlets_5.5.0-2_all.deb ... 325s Unpacking python3-traitlets (5.5.0-2) ... 325s Selecting previously unselected package python3-matplotlib-inline. 325s Preparing to unpack .../70-python3-matplotlib-inline_0.1.6-2_all.deb ... 325s Unpacking python3-matplotlib-inline (0.1.6-2) ... 326s Selecting previously unselected package python3-ptyprocess. 326s Preparing to unpack .../71-python3-ptyprocess_0.7.0-5_all.deb ... 326s Unpacking python3-ptyprocess (0.7.0-5) ... 326s Selecting previously unselected package python3-pexpect. 326s Preparing to unpack .../72-python3-pexpect_4.9-2_all.deb ... 326s Unpacking python3-pexpect (4.9-2) ... 326s Selecting previously unselected package python3-wcwidth. 326s Preparing to unpack .../73-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 326s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 326s Selecting previously unselected package python3-prompt-toolkit. 326s Preparing to unpack .../74-python3-prompt-toolkit_3.0.43-1_all.deb ... 326s Unpacking python3-prompt-toolkit (3.0.43-1) ... 326s Selecting previously unselected package python3-pure-eval. 326s Preparing to unpack .../75-python3-pure-eval_0.2.2-1_all.deb ... 326s Unpacking python3-pure-eval (0.2.2-1) ... 326s Selecting previously unselected package python3-stack-data. 326s Preparing to unpack .../76-python3-stack-data_0.6.3-1_all.deb ... 326s Unpacking python3-stack-data (0.6.3-1) ... 326s Selecting previously unselected package python3-ipython. 326s Preparing to unpack .../77-python3-ipython_8.20.0-1_all.deb ... 326s Unpacking python3-ipython (8.20.0-1) ... 326s Selecting previously unselected package python3-kiwisolver. 326s Preparing to unpack .../78-python3-kiwisolver_1.4.4-2_arm64.deb ... 326s Unpacking python3-kiwisolver (1.4.4-2) ... 326s Selecting previously unselected package libopenjp2-7:arm64. 326s Preparing to unpack .../79-libopenjp2-7_2.5.0-2_arm64.deb ... 326s Unpacking libopenjp2-7:arm64 (2.5.0-2) ... 326s Selecting previously unselected package python3-pil:arm64. 326s Preparing to unpack .../80-python3-pil_10.2.0-1_arm64.deb ... 326s Unpacking python3-pil:arm64 (10.2.0-1) ... 326s Selecting previously unselected package python3-tk:arm64. 326s Preparing to unpack .../81-python3-tk_3.11.5-1_arm64.deb ... 326s Unpacking python3-tk:arm64 (3.11.5-1) ... 326s Selecting previously unselected package python3-pil.imagetk:arm64. 326s Preparing to unpack .../82-python3-pil.imagetk_10.2.0-1_arm64.deb ... 326s Unpacking python3-pil.imagetk:arm64 (10.2.0-1) ... 327s Selecting previously unselected package python3-packaging. 327s Preparing to unpack .../83-python3-packaging_23.2-1_all.deb ... 327s Unpacking python3-packaging (23.2-1) ... 327s Selecting previously unselected package python3-matplotlib. 327s Preparing to unpack .../84-python3-matplotlib_3.6.3-1ubuntu3_arm64.deb ... 327s Unpacking python3-matplotlib (3.6.3-1ubuntu3) ... 327s Selecting previously unselected package python3-natsort. 327s Preparing to unpack .../85-python3-natsort_8.0.2-2_all.deb ... 327s Unpacking python3-natsort (8.0.2-2) ... 327s Selecting previously unselected package python3-pandas-lib:arm64. 327s Preparing to unpack .../86-python3-pandas-lib_2.1.4+dfsg-4ubuntu2_arm64.deb ... 327s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-4ubuntu2) ... 328s Selecting previously unselected package python3-pandas. 328s Preparing to unpack .../87-python3-pandas_2.1.4+dfsg-4ubuntu2_all.deb ... 328s Unpacking python3-pandas (2.1.4+dfsg-4ubuntu2) ... 328s Selecting previously unselected package python3-pluggy. 328s Preparing to unpack .../88-python3-pluggy_1.4.0-1_all.deb ... 328s Unpacking python3-pluggy (1.4.0-1) ... 328s Selecting previously unselected package python3-pytest. 328s Preparing to unpack .../89-python3-pytest_7.4.4-1_all.deb ... 328s Unpacking python3-pytest (7.4.4-1) ... 328s Selecting previously unselected package python3-skbio. 328s Preparing to unpack .../90-python3-skbio_0.5.9-4_arm64.deb ... 328s Unpacking python3-skbio (0.5.9-4) ... 329s Selecting previously unselected package autopkgtest-satdep. 329s Preparing to unpack .../91-1-autopkgtest-satdep.deb ... 329s Unpacking autopkgtest-satdep (0) ... 329s Setting up libgraphite2-3:arm64 (1.3.14-2) ... 329s Setting up liblcms2-2:arm64 (2.14-2) ... 329s Setting up python3-iniconfig (1.1.1-2) ... 329s Setting up libsharpyuv0:arm64 (1.3.2-0.4) ... 329s Setting up python3-pure-eval (0.2.2-1) ... 329s Setting up liblerc4:arm64 (4.0.0+ds-4ubuntu1) ... 329s Setting up libxrender1:arm64 (1:0.9.10-1.1) ... 329s Setting up python3-parso (0.8.3-1) ... 330s Setting up python3-lz4 (4.0.2+dfsg-1build2) ... 330s Setting up python3-asttokens (2.4.1-1) ... 330s Setting up python3-unicodedata2 (15.1.0+ds-1) ... 330s Setting up fonts-lyx (2.4.0~RC3-1) ... 330s Setting up x11-common (1:7.7+23ubuntu2) ... 331s Setting up libdeflate0:arm64 (1.19-1) ... 331s Setting up libqhull-r8.0:arm64 (2020.2-6) ... 331s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 331s Setting up libjbig0:arm64 (2.1-6.1ubuntu1) ... 331s Setting up libaec0:arm64 (1.1.2-1) ... 331s Setting up python3-natsort (8.0.2-2) ... 332s Setting up unicode-data (15.1.0-1) ... 332s Setting up python3-decorator (5.1.1-5) ... 332s Setting up libblas3:arm64 (3.12.0-3) ... 332s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 332s Setting up python3-packaging (23.2-1) ... 332s Setting up python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 333s Setting up python3-executing (2.0.1-0.1) ... 333s Setting up python3-brotli (1.1.0-2) ... 333s Setting up liblzf1:arm64 (3.6-4) ... 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[03:23:49]: test testsuite: preparing testbed 404s Reading package lists... 404s Building dependency tree... 404s Reading state information... 405s Starting pkgProblemResolver with broken count: 0 405s Starting 2 pkgProblemResolver with broken count: 0 405s Done 406s The following NEW packages will be installed: 406s autopkgtest-satdep 406s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 406s Need to get 0 B/712 B of archives. 406s After this operation, 0 B of additional disk space will be used. 406s Get:1 /tmp/autopkgtest.QcvHYo/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 407s Selecting previously unselected package autopkgtest-satdep. 407s (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 ... 88060 files and directories currently installed.) 407s Preparing to unpack .../2-autopkgtest-satdep.deb ... 407s Unpacking autopkgtest-satdep (0) ... 407s Setting up autopkgtest-satdep (0) ... 411s (Reading database ... 88060 files and directories currently installed.) 411s Removing autopkgtest-satdep (0) ... 412s autopkgtest [03:24:00]: test testsuite: [----------------------- 412s + 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 {} ; 412s + 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 {} ; 412s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 419s ============================= test session starts ============================== 419s platform linux -- Python 3.12.2, pytest-7.4.4, pluggy-1.4.0 419s rootdir: /tmp/autopkgtest.QcvHYo/autopkgtest_tmp 419s collected 2390 items 419s 420s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 420s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 420s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 421s ........................................................................ 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[ 24%] 433s [ 24%] 433s skbio/diversity/tests/test_util.py ........... [ 24%] 433s skbio/io/format/tests/test_base.py ................................ [ 26%] 433s skbio/io/format/tests/test_binary_dm.py ......... [ 26%] 433s skbio/io/format/tests/test_blast6.py ........... [ 26%] 434s skbio/io/format/tests/test_blast7.py .............. [ 27%] 434s skbio/io/format/tests/test_clustal.py ............. [ 27%] 439s skbio/io/format/tests/test_embl.py ............................... [ 29%] 439s skbio/io/format/tests/test_emptyfile.py .. [ 29%] 453s skbio/io/format/tests/test_fasta.py ................ [ 30%] 464s skbio/io/format/tests/test_fastq.py ............... [ 30%] 466s skbio/io/format/tests/test_genbank.py ..................... [ 31%] 467s skbio/io/format/tests/test_gff3.py ........................ [ 32%] 467s skbio/io/format/tests/test_lsmat.py ....... [ 32%] 467s skbio/io/format/tests/test_newick.py ....... [ 33%] 469s skbio/io/format/tests/test_ordination.py ..... [ 33%] 471s skbio/io/format/tests/test_phylip.py ....... [ 33%] 472s skbio/io/format/tests/test_qseq.py ...... [ 33%] 472s skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 34%] 474s skbio/io/format/tests/test_stockholm.py ................................ [ 35%] 475s ........................................... [ 37%] 475s skbio/io/format/tests/test_taxdump.py ...... [ 37%] 475s skbio/io/tests/test_iosources.py .......... [ 37%] 475s skbio/io/tests/test_registry.py ........................................ [ 39%] 476s ...................................................... [ 41%] 479s skbio/io/tests/test_util.py .......................................XXsss [ 43%] 483s sssssssssssssssssssssssssss..................................xx......... [ 46%] 490s .........................xx..................................xx......... [ 49%] 493s .........................xx..... [ 51%] 497s skbio/metadata/tests/test_intersection.py ............... [ 51%] 497s skbio/metadata/tests/test_interval.py .................................. [ 53%] 497s ..................................... [ 54%] 497s skbio/metadata/tests/test_mixin.py ..................................... [ 56%] 497s ............................................................. [ 58%] 497s skbio/sequence/tests/test_distance.py .......................... [ 59%] 497s skbio/sequence/tests/test_dna.py .... [ 59%] 497s skbio/sequence/tests/test_genetic_code.py .......................... [ 61%] 497s skbio/sequence/tests/test_grammared_sequence.py ........................ [ 62%] 497s ................... [ 62%] 498s skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 63%] 498s ....... [ 64%] 498s skbio/sequence/tests/test_protein.py .......... [ 64%] 498s skbio/sequence/tests/test_rna.py .... [ 64%] 498s skbio/sequence/tests/test_sequence.py .................................. [ 66%] 498s ........................................................................ [ 69%] 498s ........................................................................ [ 72%] 499s ........................................................................ [ 75%] 499s ....... [ 75%] 499s skbio/stats/distance/tests/test_anosim.py .... [ 75%] 500s skbio/stats/distance/tests/test_base.py ................................ [ 76%] 501s ................................................................... [ 79%] 520s skbio/stats/distance/tests/test_bioenv.py ................. [ 80%] 527s skbio/stats/distance/tests/test_mantel.py .............................. [ 81%] 528s .............. [ 82%] 528s skbio/stats/distance/tests/test_permanova.py .... [ 82%] 542s skbio/stats/distance/tests/test_permdisp.py ............. [ 82%] 542s skbio/stats/evolve/tests/test_hommola.py ............ [ 83%] 542s skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%] 542s ..... [ 83%] 542s skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 84%] 544s skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%] 544s [ 84%] 544s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 84%] 545s ....... [ 85%] 545s skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 85%] 545s skbio/stats/ordination/tests/test_util.py .......... [ 85%] 545s skbio/stats/tests/test_composition.py .................................. [ 87%] 546s ............................... [ 88%] 547s skbio/stats/tests/test_gradient.py .......................... [ 89%] 547s skbio/stats/tests/test_misc.py ... [ 89%] 554s skbio/stats/tests/test_power.py ........................................ [ 91%] 555s ... [ 91%] 555s skbio/stats/tests/test_subsample.py ............ [ 92%] 555s skbio/tests/test_base.py ..... [ 92%] 555s skbio/tests/test_workflow.py ................. [ 92%] 555s skbio/tree/tests/test_majority_rule.py ...... [ 93%] 555s skbio/tree/tests/test_nj.py ........... [ 93%] 556s skbio/tree/tests/test_tree.py .......................................... [ 95%] 556s ................................................... [ 97%] 556s skbio/util/tests/test_decorator.py ....................... [ 98%] 556s skbio/util/tests/test_misc.py .................... [ 99%] 556s skbio/util/tests/test_testing.py ............... [100%] 556s 556s =============================== warnings summary =============================== 556s ../../../usr/lib/python3/dist-packages/dateutil/tz/tz.py:37 556s /usr/lib/python3/dist-packages/dateutil/tz/tz.py:37: DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC). 556s EPOCH = datetime.datetime.utcfromtimestamp(0) 556s 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 556s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 556s /tmp/autopkgtest.QcvHYo/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 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 556s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 556s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 556s /tmp/autopkgtest.QcvHYo/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]` 556s df['bar'][0].append(42) 556s 556s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 556s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 556s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 556s /tmp/autopkgtest.QcvHYo/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]` 556s df['bar'][0].append(42) 556s 556s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 556s gap_freqs /= length 556s 556s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 556s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 556s 556s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 556s freqs = counts / counts.sum() 556s 556s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 556s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 556s 556s skbio/diversity/tests/test_block.py: 3 warnings 556s skbio/diversity/tests/test_driver.py: 9 warnings 556s /tmp/autopkgtest.QcvHYo/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. 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input 556s /usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison 556s return imag(x) == 0 556s 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 556s /tmp/autopkgtest.QcvHYo/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 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 556s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 556s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 556s /tmp/autopkgtest.QcvHYo/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 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 556s /tmp/autopkgtest.QcvHYo/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 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 556s obs_counts = obs_counts / len(self) 556s 556s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 556s warnings.warn(ConstantInputWarning()) 556s 556s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 556s warnings.warn(ConstantInputWarning()) 556s 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 556s /tmp/autopkgtest.QcvHYo/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 -13.541846544269621 and the largest is 16.587201374785895. 556s warn( 556s 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 556s /tmp/autopkgtest.QcvHYo/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 -15.629533932395201 and the largest is 20.903154277938906. 556s warn( 556s 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 556s proportion_explained = eigvals / sum_eigenvalues 556s 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 556s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 556s /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 556s warnings.warn(stats.ConstantInputWarning(msg)) 556s 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 556s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 556s /tmp/autopkgtest.QcvHYo/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 -0.007758325147780542 and the largest is 2.7077929489469237. 556s warn( 556s 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 556s /tmp/autopkgtest.QcvHYo/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. 556s fig.tight_layout() 556s 556s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 556s plot = scatter_fn(c=point_colors, cmap=cmap) 556s 556s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 556s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 556s return self.run(*args, **kwds) 556s 556s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 556s /tmp/autopkgtest.QcvHYo/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]` 556s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 556s 556s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 556s /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. 556s res = hypotest_fun_out(*samples, **kwds) 556s 556s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 556s X_log = np.log(mat) 556s 556s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 556s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2699: RuntimeWarning: invalid value encountered in subtract 556s X -= avg[:, None] 556s 556s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 556s /tmp/autopkgtest.QcvHYo/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 556s x = np.log(x) 556s 556s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 556s /usr/lib/python3/dist-packages/numpy/core/_methods.py:236: RuntimeWarning: invalid value encountered in subtract 556s x = asanyarray(arr - arrmean) 556s 556s skbio/stats/tests/test_gradient.py: 13 warnings 556s /tmp/autopkgtest.QcvHYo/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]` 556s np.abs((w_vector[i] - w_vector[i-1])) 556s 556s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 556s /tmp/autopkgtest.QcvHYo/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. 556s trajectories.loc[idx] = ( 556s 556s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 556s /tmp/autopkgtest.QcvHYo/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(). 556s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 556s 556s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 556s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 94 warnings in 143.72s (0:02:23) = 559s autopkgtest [03:26:27]: test testsuite: -----------------------] 559s autopkgtest [03:26:27]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 559s testsuite PASS 560s autopkgtest [03:26:28]: @@@@@@@@@@@@@@@@@@@@ summary 560s import-skbio PASS 560s testsuite PASS 574s Creating nova instance adt-noble-arm64-python-skbio-20240324-031708-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240323.img (UUID 5063c5cd-2683-4ea1-9e65-62351adfb1a7)...