0s autopkgtest [13:19:04]: starting date and time: 2024-06-08 13:19:04+0000 0s autopkgtest [13:19:04]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [13:19:04]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.h6ifdj0q/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@bos03-arm64-44.secgroup --name adt-oracular-arm64-python-skbio-20240608-131904-juju-7f2275-prod-proposed-migration-environment-2-71d73ab4-78ee-4564-b8a5-d9036624d3da --image adt/ubuntu-oracular-arm64-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/ 808s autopkgtest [13:32:32]: testbed dpkg architecture: arm64 808s autopkgtest [13:32:32]: testbed apt version: 2.9.3 808s autopkgtest [13:32:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 809s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 809s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.2 kB] 809s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [338 kB] 809s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 809s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2420 B] 809s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [67.9 kB] 809s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [31.8 kB] 809s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [306 kB] 809s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [9556 B] 809s Fetched 918 kB in 1s (962 kB/s) 809s Reading package lists... 812s Reading package lists... 812s Building dependency tree... 812s Reading state information... 813s Calculating upgrade... 813s The following packages will be upgraded: 813s bash 814s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 814s Need to get 781 kB of archives. 814s After this operation, 0 B of additional disk space will be used. 814s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 bash arm64 5.2.21-2.1ubuntu1 [781 kB] 815s Fetched 781 kB in 1s (563 kB/s) 815s (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 ... 78200 files and directories currently installed.) 815s Preparing to unpack .../bash_5.2.21-2.1ubuntu1_arm64.deb ... 815s Unpacking bash (5.2.21-2.1ubuntu1) over (5.2.21-2ubuntu5) ... 815s Setting up bash (5.2.21-2.1ubuntu1) ... 815s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 815s Processing triggers for debianutils (5.18) ... 815s Processing triggers for install-info (7.1-3build2) ... 815s Processing triggers for man-db (2.12.1-1) ... 817s Reading package lists... 817s Building dependency tree... 817s Reading state information... 817s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 819s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 819s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 819s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 819s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 820s Reading package lists... 820s Reading package lists... 821s Building dependency tree... 821s Reading state information... 821s Calculating upgrade... 822s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 822s Reading package lists... 822s Building dependency tree... 822s Reading state information... 823s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 826s autopkgtest [13:32:50]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 826s autopkgtest [13:32:50]: @@@@@@@@@@@@@@@@@@@@ apt-source python-skbio 830s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (dsc) [2803 B] 830s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (tar) [3559 kB] 830s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-skbio 0.5.9-4build1 (diff) [15.7 kB] 830s gpgv: Signature made Wed Apr 10 15:30:06 2024 UTC 830s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 830s gpgv: Can't check signature: No public key 830s dpkg-source: warning: cannot verify inline signature for ./python-skbio_0.5.9-4build1.dsc: no acceptable signature found 830s autopkgtest [13:32:54]: testing package python-skbio version 0.5.9-4build1 830s autopkgtest [13:32:54]: build not needed 831s autopkgtest [13:32:55]: test import-skbio: preparing testbed 832s Reading package lists... 833s Building dependency tree... 833s Reading state information... 833s Starting pkgProblemResolver with broken count: 0 833s Starting 2 pkgProblemResolver with broken count: 0 833s Done 834s The following additional packages will be installed: 834s blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 libgraphite2-3 834s libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libjs-jquery 834s libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 liblzf1 libopenjp2-7 834s libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 libtk8.6 libwebpdemux2 834s libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 python-matplotlib-data 834s python3-appdirs python3-asttokens python3-brotli python3-contourpy 834s python3-cycler python3-dateutil python3-decorator python3-executing 834s python3-fonttools python3-fs python3-h5py python3-h5py-serial 834s python3-hdmedians python3-iniconfig python3-ipython python3-jedi 834s python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 834s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 834s python3-packaging python3-pandas python3-pandas-lib python3-parso 834s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 834s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 834s python3-scipy python3-setuptools python3-skbio python3-stack-data 834s python3-sympy python3-tk python3-traitlets python3-typeshed python3-ufolib2 834s python3-unicodedata2 python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 834s Suggested packages: 834s blt-demo libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python-cycler-doc 834s python-h5py-doc python-ipython-doc python-lxml-doc cm-super-minimal dvipng 834s ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 834s librsvg2-common python3-cairocffi python3-gi-cairo python3-gobject 834s python3-pyqt5 python3-sip python3-tornado texlive-extra-utils 834s texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc 834s gfortran python-numpy-doc python3-dev python-pandas-doc python3-statsmodels 834s python-pexpect-doc python-pil-doc python-scipy-doc python-setuptools-doc 834s python-skbio-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg 834s Recommended packages: 834s javascript-common python3-bs4 python3-cssselect python3-html5lib 834s python3-bottleneck python3-numexpr python3-odf python3-openpyxl 834s python3-tables python3-olefile g++ | c++-compiler isympy-common 834s The following NEW packages will be installed: 834s autopkgtest-satdep blt fonts-lyx libaec0 libblas3 libgfortran5 libgomp1 834s libgraphite2-3 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 834s libimagequant0 libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 834s liblzf1 libopenjp2-7 libqhull-r8.0 libraqm0 libssw0 libsz2 libtcl8.6 834s libtk8.6 libwebpdemux2 libwebpmux3 libxft2 libxrender1 libxslt1.1 libxss1 834s python-matplotlib-data python3-appdirs python3-asttokens python3-brotli 834s python3-contourpy python3-cycler python3-dateutil python3-decorator 834s python3-executing python3-fonttools python3-fs python3-h5py 834s python3-h5py-serial python3-hdmedians python3-iniconfig python3-ipython 834s python3-jedi python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib 834s python3-matplotlib-inline python3-mpmath python3-natsort python3-numpy 834s python3-packaging python3-pandas python3-pandas-lib python3-parso 834s python3-pexpect python3-pil python3-pil.imagetk python3-pluggy 834s python3-prompt-toolkit python3-ptyprocess python3-pure-eval python3-pytest 834s python3-scipy python3-setuptools python3-skbio python3-stack-data 834s python3-sympy python3-tk python3-traitlets python3-typeshed python3-ufolib2 834s python3-unicodedata2 python3-wcwidth tk8.6-blt2.5 unicode-data x11-common 835s 0 upgraded, 82 newly installed, 0 to remove and 0 not upgraded. 835s Need to get 66.7 MB/66.7 MB of archives. 835s After this operation, 309 MB of additional disk space will be used. 835s Get:1 /tmp/autopkgtest.oIisQn/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 837s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libtcl8.6 arm64 8.6.14+dfsg-1build1 [978 kB] 838s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libxrender1 arm64 1:0.9.10-1.1build1 [18.8 kB] 838s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 libxft2 arm64 2.3.6-1build1 [44.1 kB] 838s Get:5 http://ftpmaster.internal/ubuntu oracular/main arm64 x11-common all 1:7.7+23ubuntu3 [21.7 kB] 838s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 libxss1 arm64 1:1.2.3-1build3 [7244 B] 838s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 libtk8.6 arm64 8.6.14-1build1 [767 kB] 838s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-7build1 [618 kB] 838s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 blt arm64 2.5.3+dfsg-7build1 [4840 B] 838s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 fonts-lyx all 2.4.0-1 [171 kB] 838s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 libaec0 arm64 1.1.3-1 [22.0 kB] 838s Get:12 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 838s Get:13 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 838s Get:14 http://ftpmaster.internal/ubuntu oracular/main arm64 libgomp1 arm64 14.1.0-1ubuntu1 [144 kB] 838s Get:15 http://ftpmaster.internal/ubuntu oracular/main arm64 libgraphite2-3 arm64 1.3.14-2build1 [70.8 kB] 838s Get:16 http://ftpmaster.internal/ubuntu oracular/main arm64 libharfbuzz0b arm64 8.3.0-2build2 [463 kB] 838s Get:17 http://ftpmaster.internal/ubuntu oracular/universe arm64 libsz2 arm64 1.1.3-1 [5254 B] 838s Get:18 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-103-1t64 arm64 1.10.10+repack-3.1ubuntu4 [1192 kB] 838s Get:19 http://ftpmaster.internal/ubuntu oracular/universe arm64 libhdf5-hl-100t64 arm64 1.10.10+repack-3.1ubuntu4 [55.8 kB] 838s Get:20 http://ftpmaster.internal/ubuntu oracular/main arm64 libimagequant0 arm64 2.18.0-1build1 [37.1 kB] 838s Get:21 http://ftpmaster.internal/ubuntu oracular/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB] 838s Get:22 http://ftpmaster.internal/ubuntu oracular/universe arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB] 838s Get:23 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 838s Get:24 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 838s Get:25 http://ftpmaster.internal/ubuntu oracular/main arm64 liblcms2-2 arm64 2.14-2build1 [161 kB] 838s Get:26 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblzf1 arm64 3.6-4 [7426 B] 838s Get:27 http://ftpmaster.internal/ubuntu oracular/universe arm64 libqhull-r8.0 arm64 2020.2-6build1 [189 kB] 838s Get:28 http://ftpmaster.internal/ubuntu oracular/main arm64 libraqm0 arm64 0.10.1-1build1 [14.7 kB] 838s Get:29 http://ftpmaster.internal/ubuntu oracular/universe arm64 libssw0 arm64 1.1-14build1 [21.4 kB] 838s Get:30 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpdemux2 arm64 1.4.0-0.1 [12.3 kB] 838s Get:31 http://ftpmaster.internal/ubuntu oracular/main arm64 libwebpmux3 arm64 1.4.0-0.1 [25.1 kB] 838s Get:32 http://ftpmaster.internal/ubuntu oracular/main arm64 libxslt1.1 arm64 1.1.39-0exp1build1 [166 kB] 838s Get:33 http://ftpmaster.internal/ubuntu oracular/universe arm64 python-matplotlib-data all 3.6.3-2ubuntu1 [2937 kB] 838s Get:34 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-appdirs all 1.4.4-4 [10.9 kB] 838s Get:35 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-asttokens all 2.4.1-1 [20.9 kB] 838s Get:36 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-brotli arm64 1.1.0-2build2 [340 kB] 838s Get:37 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 838s Get:38 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-contourpy arm64 1.0.7-3 [163 kB] 838s Get:39 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-cycler all 0.12.1-1 [9716 B] 838s Get:40 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-dateutil all 2.9.0-2 [80.3 kB] 838s Get:41 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 838s Get:42 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-executing all 2.0.1-0.1 [23.3 kB] 838s Get:43 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.11.4-10 [15.0 MB] 839s Get:44 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ufolib2 all 0.16.0+dfsg1-1 [33.5 kB] 839s Get:45 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-mpmath all 1.3.0-1 [425 kB] 839s Get:46 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-sympy all 1.12-8 [3966 kB] 839s Get:47 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-fs all 2.4.16-4 [91.3 kB] 839s Get:48 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-lxml arm64 5.2.1-1 [1179 kB] 839s Get:49 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-lz4 arm64 4.0.2+dfsg-1build4 [26.7 kB] 839s Get:50 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-unicodedata2 arm64 15.1.0+ds-1build1 [362 kB] 839s Get:51 http://ftpmaster.internal/ubuntu oracular/universe arm64 unicode-data all 15.1.0-1 [8878 kB] 839s Get:52 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-fonttools arm64 4.46.0-1build2 [1398 kB] 839s Get:53 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h5py-serial arm64 3.10.0-1ubuntu3 [888 kB] 839s Get:54 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-h5py all 3.10.0-1ubuntu3 [7978 B] 839s Get:55 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-hdmedians arm64 0.14.2-5.1build1 [116 kB] 839s Get:56 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 839s Get:57 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-parso all 0.8.3-1 [67.2 kB] 839s Get:58 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-typeshed all 0.0~git20231111.6764465-3 [1274 kB] 839s Get:59 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-jedi all 0.19.1+ds1-1 [693 kB] 839s Get:60 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-traitlets all 5.5.0-2 [85.0 kB] 839s Get:61 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-matplotlib-inline all 0.1.6-2 [8784 B] 839s Get:62 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-ptyprocess all 0.7.0-5 [15.1 kB] 839s Get:63 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pexpect all 4.9-2 [48.1 kB] 839s Get:64 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-wcwidth all 0.2.5+dfsg1-1.1ubuntu1 [22.5 kB] 839s Get:65 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-prompt-toolkit all 3.0.46-1 [256 kB] 839s Get:66 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pure-eval all 0.2.2-2 [11.1 kB] 839s Get:67 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-stack-data all 0.6.3-1 [22.0 kB] 839s Get:68 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-setuptools all 68.1.2-2ubuntu1 [396 kB] 839s Get:69 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ipython all 8.20.0-1ubuntu1 [561 kB] 839s Get:70 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-kiwisolver arm64 1.4.5-1 [48.9 kB] 839s Get:71 http://ftpmaster.internal/ubuntu oracular/main arm64 libopenjp2-7 arm64 2.5.0-2build3 [171 kB] 839s Get:72 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-pil arm64 10.3.0-2 [446 kB] 839s Get:73 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-tk arm64 3.12.3-0ubuntu1 [102 kB] 839s Get:74 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pil.imagetk arm64 10.3.0-2 [9268 B] 839s Get:75 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 839s Get:76 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-matplotlib arm64 3.6.3-2ubuntu1 [5963 kB] 840s Get:77 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-natsort all 8.0.2-2 [33.8 kB] 840s Get:78 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas-lib arm64 2.1.4+dfsg-8 [4178 kB] 840s Get:79 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pandas all 2.1.4+dfsg-8 [3042 kB] 840s Get:80 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 840s Get:81 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 840s Get:82 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-skbio arm64 0.5.9-4build1 [744 kB] 841s Fetched 66.7 MB in 5s (12.6 MB/s) 841s Selecting previously unselected package libtcl8.6:arm64. 841s (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 ... 78200 files and directories currently installed.) 841s Preparing to unpack .../00-libtcl8.6_8.6.14+dfsg-1build1_arm64.deb ... 841s Unpacking libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 841s Selecting previously unselected package libxrender1:arm64. 841s Preparing to unpack .../01-libxrender1_1%3a0.9.10-1.1build1_arm64.deb ... 841s Unpacking libxrender1:arm64 (1:0.9.10-1.1build1) ... 841s Selecting previously unselected package libxft2:arm64. 841s Preparing to unpack .../02-libxft2_2.3.6-1build1_arm64.deb ... 841s Unpacking libxft2:arm64 (2.3.6-1build1) ... 841s Selecting previously unselected package x11-common. 841s Preparing to unpack .../03-x11-common_1%3a7.7+23ubuntu3_all.deb ... 841s Unpacking x11-common (1:7.7+23ubuntu3) ... 842s Selecting previously unselected package libxss1:arm64. 842s Preparing to unpack .../04-libxss1_1%3a1.2.3-1build3_arm64.deb ... 842s Unpacking libxss1:arm64 (1:1.2.3-1build3) ... 842s Selecting previously unselected package libtk8.6:arm64. 842s Preparing to unpack .../05-libtk8.6_8.6.14-1build1_arm64.deb ... 842s Unpacking libtk8.6:arm64 (8.6.14-1build1) ... 842s Selecting previously unselected package tk8.6-blt2.5. 842s Preparing to unpack .../06-tk8.6-blt2.5_2.5.3+dfsg-7build1_arm64.deb ... 842s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 842s Selecting previously unselected package blt. 842s Preparing to unpack .../07-blt_2.5.3+dfsg-7build1_arm64.deb ... 842s Unpacking blt (2.5.3+dfsg-7build1) ... 842s Selecting previously unselected package fonts-lyx. 842s Preparing to unpack .../08-fonts-lyx_2.4.0-1_all.deb ... 842s Unpacking fonts-lyx (2.4.0-1) ... 842s Selecting previously unselected package libaec0:arm64. 842s Preparing to unpack .../09-libaec0_1.1.3-1_arm64.deb ... 842s Unpacking libaec0:arm64 (1.1.3-1) ... 842s Selecting previously unselected package libblas3:arm64. 842s Preparing to unpack .../10-libblas3_3.12.0-3build1_arm64.deb ... 842s Unpacking libblas3:arm64 (3.12.0-3build1) ... 842s Selecting previously unselected package libgfortran5:arm64. 842s Preparing to unpack .../11-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 842s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 842s Selecting previously unselected package libgomp1:arm64. 842s Preparing to unpack .../12-libgomp1_14.1.0-1ubuntu1_arm64.deb ... 842s Unpacking libgomp1:arm64 (14.1.0-1ubuntu1) ... 842s Selecting previously unselected package libgraphite2-3:arm64. 842s Preparing to unpack .../13-libgraphite2-3_1.3.14-2build1_arm64.deb ... 842s Unpacking libgraphite2-3:arm64 (1.3.14-2build1) ... 842s Selecting previously unselected package libharfbuzz0b:arm64. 842s Preparing to unpack .../14-libharfbuzz0b_8.3.0-2build2_arm64.deb ... 842s Unpacking libharfbuzz0b:arm64 (8.3.0-2build2) ... 842s Selecting previously unselected package libsz2:arm64. 842s Preparing to unpack .../15-libsz2_1.1.3-1_arm64.deb ... 842s Unpacking libsz2:arm64 (1.1.3-1) ... 842s Selecting previously unselected package libhdf5-103-1t64:arm64. 842s Preparing to unpack .../16-libhdf5-103-1t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 842s Unpacking libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 842s Selecting previously unselected package libhdf5-hl-100t64:arm64. 842s Preparing to unpack .../17-libhdf5-hl-100t64_1.10.10+repack-3.1ubuntu4_arm64.deb ... 842s Unpacking libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 842s Selecting previously unselected package libimagequant0:arm64. 843s Preparing to unpack .../18-libimagequant0_2.18.0-1build1_arm64.deb ... 843s Unpacking libimagequant0:arm64 (2.18.0-1build1) ... 843s Selecting previously unselected package libjs-jquery. 843s Preparing to unpack .../19-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... 843s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 843s Selecting previously unselected package libjs-jquery-ui. 843s Preparing to unpack .../20-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... 843s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... 843s Selecting previously unselected package liblapack3:arm64. 843s Preparing to unpack .../21-liblapack3_3.12.0-3build1_arm64.deb ... 843s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 843s Selecting previously unselected package liblbfgsb0:arm64. 843s Preparing to unpack .../22-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 843s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 843s Selecting previously unselected package liblcms2-2:arm64. 843s Preparing to unpack .../23-liblcms2-2_2.14-2build1_arm64.deb ... 843s Unpacking liblcms2-2:arm64 (2.14-2build1) ... 843s Selecting previously unselected package liblzf1:arm64. 843s Preparing to unpack .../24-liblzf1_3.6-4_arm64.deb ... 843s Unpacking liblzf1:arm64 (3.6-4) ... 843s Selecting previously unselected package libqhull-r8.0:arm64. 843s Preparing to unpack .../25-libqhull-r8.0_2020.2-6build1_arm64.deb ... 843s Unpacking libqhull-r8.0:arm64 (2020.2-6build1) ... 843s Selecting previously unselected package libraqm0:arm64. 843s Preparing to unpack .../26-libraqm0_0.10.1-1build1_arm64.deb ... 843s Unpacking libraqm0:arm64 (0.10.1-1build1) ... 844s Selecting previously unselected package libssw0:arm64. 844s Preparing to unpack .../27-libssw0_1.1-14build1_arm64.deb ... 844s Unpacking libssw0:arm64 (1.1-14build1) ... 844s Selecting previously unselected package libwebpdemux2:arm64. 844s Preparing to unpack .../28-libwebpdemux2_1.4.0-0.1_arm64.deb ... 844s Unpacking libwebpdemux2:arm64 (1.4.0-0.1) ... 844s Selecting previously unselected package libwebpmux3:arm64. 844s Preparing to unpack .../29-libwebpmux3_1.4.0-0.1_arm64.deb ... 844s Unpacking libwebpmux3:arm64 (1.4.0-0.1) ... 844s Selecting previously unselected package libxslt1.1:arm64. 844s Preparing to unpack .../30-libxslt1.1_1.1.39-0exp1build1_arm64.deb ... 844s Unpacking libxslt1.1:arm64 (1.1.39-0exp1build1) ... 844s Selecting previously unselected package python-matplotlib-data. 844s Preparing to unpack .../31-python-matplotlib-data_3.6.3-2ubuntu1_all.deb ... 844s Unpacking python-matplotlib-data (3.6.3-2ubuntu1) ... 844s Selecting previously unselected package python3-appdirs. 844s Preparing to unpack .../32-python3-appdirs_1.4.4-4_all.deb ... 844s Unpacking python3-appdirs (1.4.4-4) ... 845s Selecting previously unselected package python3-asttokens. 845s Preparing to unpack .../33-python3-asttokens_2.4.1-1_all.deb ... 845s Unpacking python3-asttokens (2.4.1-1) ... 845s Selecting previously unselected package python3-brotli. 845s Preparing to unpack .../34-python3-brotli_1.1.0-2build2_arm64.deb ... 845s Unpacking python3-brotli (1.1.0-2build2) ... 845s Selecting previously unselected package python3-numpy. 845s Preparing to unpack .../35-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 845s Unpacking python3-numpy (1:1.26.4+ds-10) ... 845s Selecting previously unselected package python3-contourpy. 845s Preparing to unpack .../36-python3-contourpy_1.0.7-3_arm64.deb ... 845s Unpacking python3-contourpy (1.0.7-3) ... 845s Selecting previously unselected package python3-cycler. 845s Preparing to unpack .../37-python3-cycler_0.12.1-1_all.deb ... 845s Unpacking python3-cycler (0.12.1-1) ... 845s Selecting previously unselected package python3-dateutil. 845s Preparing to unpack .../38-python3-dateutil_2.9.0-2_all.deb ... 845s Unpacking python3-dateutil (2.9.0-2) ... 845s Selecting previously unselected package python3-decorator. 845s Preparing to unpack .../39-python3-decorator_5.1.1-5_all.deb ... 845s Unpacking python3-decorator (5.1.1-5) ... 845s Selecting previously unselected package python3-executing. 845s Preparing to unpack .../40-python3-executing_2.0.1-0.1_all.deb ... 845s Unpacking python3-executing (2.0.1-0.1) ... 845s Selecting previously unselected package python3-scipy. 846s Preparing to unpack .../41-python3-scipy_1.11.4-10_arm64.deb ... 846s Unpacking python3-scipy (1.11.4-10) ... 846s Selecting previously unselected package python3-ufolib2. 846s Preparing to unpack .../42-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... 846s Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... 846s Selecting previously unselected package python3-mpmath. 846s Preparing to unpack .../43-python3-mpmath_1.3.0-1_all.deb ... 846s Unpacking python3-mpmath (1.3.0-1) ... 847s Selecting previously unselected package python3-sympy. 847s Preparing to unpack .../44-python3-sympy_1.12-8_all.deb ... 847s Unpacking python3-sympy (1.12-8) ... 847s Selecting previously unselected package python3-fs. 847s Preparing to unpack .../45-python3-fs_2.4.16-4_all.deb ... 847s Unpacking python3-fs (2.4.16-4) ... 847s Selecting previously unselected package python3-lxml:arm64. 847s Preparing to unpack .../46-python3-lxml_5.2.1-1_arm64.deb ... 847s Unpacking python3-lxml:arm64 (5.2.1-1) ... 847s Selecting previously unselected package python3-lz4. 847s Preparing to unpack .../47-python3-lz4_4.0.2+dfsg-1build4_arm64.deb ... 847s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ... 847s Selecting previously unselected package python3-unicodedata2. 847s Preparing to unpack .../48-python3-unicodedata2_15.1.0+ds-1build1_arm64.deb ... 847s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ... 847s Selecting previously unselected package unicode-data. 847s Preparing to unpack .../49-unicode-data_15.1.0-1_all.deb ... 847s Unpacking unicode-data (15.1.0-1) ... 847s Selecting previously unselected package python3-fonttools. 847s Preparing to unpack .../50-python3-fonttools_4.46.0-1build2_arm64.deb ... 847s Unpacking python3-fonttools (4.46.0-1build2) ... 847s Selecting previously unselected package python3-h5py-serial. 847s Preparing to unpack .../51-python3-h5py-serial_3.10.0-1ubuntu3_arm64.deb ... 847s Unpacking python3-h5py-serial (3.10.0-1ubuntu3) ... 847s Selecting previously unselected package python3-h5py. 848s Preparing to unpack .../52-python3-h5py_3.10.0-1ubuntu3_all.deb ... 848s Unpacking python3-h5py (3.10.0-1ubuntu3) ... 848s Selecting previously unselected package python3-hdmedians. 848s Preparing to unpack .../53-python3-hdmedians_0.14.2-5.1build1_arm64.deb ... 848s Unpacking python3-hdmedians (0.14.2-5.1build1) ... 848s Selecting previously unselected package python3-iniconfig. 848s Preparing to unpack .../54-python3-iniconfig_1.1.1-2_all.deb ... 848s Unpacking python3-iniconfig (1.1.1-2) ... 848s Selecting previously unselected package python3-parso. 848s Preparing to unpack .../55-python3-parso_0.8.3-1_all.deb ... 848s Unpacking python3-parso (0.8.3-1) ... 848s Selecting previously unselected package python3-typeshed. 848s Preparing to unpack .../56-python3-typeshed_0.0~git20231111.6764465-3_all.deb ... 848s Unpacking python3-typeshed (0.0~git20231111.6764465-3) ... 848s Selecting previously unselected package python3-jedi. 848s Preparing to unpack .../57-python3-jedi_0.19.1+ds1-1_all.deb ... 848s Unpacking python3-jedi (0.19.1+ds1-1) ... 848s Selecting previously unselected package python3-traitlets. 848s Preparing to unpack .../58-python3-traitlets_5.5.0-2_all.deb ... 848s Unpacking python3-traitlets (5.5.0-2) ... 848s Selecting previously unselected package python3-matplotlib-inline. 849s Preparing to unpack .../59-python3-matplotlib-inline_0.1.6-2_all.deb ... 849s Unpacking python3-matplotlib-inline (0.1.6-2) ... 849s Selecting previously unselected package python3-ptyprocess. 849s Preparing to unpack .../60-python3-ptyprocess_0.7.0-5_all.deb ... 849s Unpacking python3-ptyprocess (0.7.0-5) ... 849s Selecting previously unselected package python3-pexpect. 849s Preparing to unpack .../61-python3-pexpect_4.9-2_all.deb ... 849s Unpacking python3-pexpect (4.9-2) ... 849s Selecting previously unselected package python3-wcwidth. 849s Preparing to unpack .../62-python3-wcwidth_0.2.5+dfsg1-1.1ubuntu1_all.deb ... 849s Unpacking python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 849s Selecting previously unselected package python3-prompt-toolkit. 849s Preparing to unpack .../63-python3-prompt-toolkit_3.0.46-1_all.deb ... 849s Unpacking python3-prompt-toolkit (3.0.46-1) ... 849s Selecting previously unselected package python3-pure-eval. 849s Preparing to unpack .../64-python3-pure-eval_0.2.2-2_all.deb ... 849s Unpacking python3-pure-eval (0.2.2-2) ... 849s Selecting previously unselected package python3-stack-data. 849s Preparing to unpack .../65-python3-stack-data_0.6.3-1_all.deb ... 849s Unpacking python3-stack-data (0.6.3-1) ... 849s Selecting previously unselected package python3-setuptools. 849s Preparing to unpack .../66-python3-setuptools_68.1.2-2ubuntu1_all.deb ... 849s Unpacking python3-setuptools (68.1.2-2ubuntu1) ... 849s Selecting previously unselected package python3-ipython. 849s Preparing to unpack .../67-python3-ipython_8.20.0-1ubuntu1_all.deb ... 849s Unpacking python3-ipython (8.20.0-1ubuntu1) ... 849s Selecting previously unselected package python3-kiwisolver. 849s Preparing to unpack .../68-python3-kiwisolver_1.4.5-1_arm64.deb ... 849s Unpacking python3-kiwisolver (1.4.5-1) ... 849s Selecting previously unselected package libopenjp2-7:arm64. 849s Preparing to unpack .../69-libopenjp2-7_2.5.0-2build3_arm64.deb ... 849s Unpacking libopenjp2-7:arm64 (2.5.0-2build3) ... 849s Selecting previously unselected package python3-pil:arm64. 849s Preparing to unpack .../70-python3-pil_10.3.0-2_arm64.deb ... 849s Unpacking python3-pil:arm64 (10.3.0-2) ... 849s Selecting previously unselected package python3-tk:arm64. 849s Preparing to unpack .../71-python3-tk_3.12.3-0ubuntu1_arm64.deb ... 849s Unpacking python3-tk:arm64 (3.12.3-0ubuntu1) ... 850s Selecting previously unselected package python3-pil.imagetk:arm64. 850s Preparing to unpack .../72-python3-pil.imagetk_10.3.0-2_arm64.deb ... 850s Unpacking python3-pil.imagetk:arm64 (10.3.0-2) ... 850s Selecting previously unselected package python3-packaging. 850s Preparing to unpack .../73-python3-packaging_24.0-1_all.deb ... 850s Unpacking python3-packaging (24.0-1) ... 850s Selecting previously unselected package python3-matplotlib. 850s Preparing to unpack .../74-python3-matplotlib_3.6.3-2ubuntu1_arm64.deb ... 850s Unpacking python3-matplotlib (3.6.3-2ubuntu1) ... 850s Selecting previously unselected package python3-natsort. 850s Preparing to unpack .../75-python3-natsort_8.0.2-2_all.deb ... 850s Unpacking python3-natsort (8.0.2-2) ... 850s Selecting previously unselected package python3-pandas-lib:arm64. 850s Preparing to unpack .../76-python3-pandas-lib_2.1.4+dfsg-8_arm64.deb ... 850s Unpacking python3-pandas-lib:arm64 (2.1.4+dfsg-8) ... 850s Selecting previously unselected package python3-pandas. 850s Preparing to unpack .../77-python3-pandas_2.1.4+dfsg-8_all.deb ... 850s Unpacking python3-pandas (2.1.4+dfsg-8) ... 851s Selecting previously unselected package python3-pluggy. 851s Preparing to unpack .../78-python3-pluggy_1.5.0-1_all.deb ... 851s Unpacking python3-pluggy (1.5.0-1) ... 851s Selecting previously unselected package python3-pytest. 851s Preparing to unpack .../79-python3-pytest_8.2.2-1ubuntu1_all.deb ... 851s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 851s Selecting previously unselected package python3-skbio. 851s Preparing to unpack .../80-python3-skbio_0.5.9-4build1_arm64.deb ... 851s Unpacking python3-skbio (0.5.9-4build1) ... 851s Selecting previously unselected package autopkgtest-satdep. 851s Preparing to unpack .../81-1-autopkgtest-satdep.deb ... 851s Unpacking autopkgtest-satdep (0) ... 851s Setting up libgraphite2-3:arm64 (1.3.14-2build1) ... 851s Setting up liblcms2-2:arm64 (2.14-2build1) ... 851s Setting up python3-iniconfig (1.1.1-2) ... 852s Setting up python3-pure-eval (0.2.2-2) ... 852s Setting up python3-setuptools (68.1.2-2ubuntu1) ... 852s Setting up libxrender1:arm64 (1:0.9.10-1.1build1) ... 852s Setting up python3-parso (0.8.3-1) ... 853s Setting up python3-lz4 (4.0.2+dfsg-1build4) ... 853s Setting up python3-asttokens (2.4.1-1) ... 853s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ... 853s Setting up fonts-lyx (2.4.0-1) ... 853s Setting up libwebpdemux2:arm64 (1.4.0-0.1) ... 853s Setting up x11-common (1:7.7+23ubuntu3) ... 854s Setting up libqhull-r8.0:arm64 (2020.2-6build1) ... 854s Setting up libgomp1:arm64 (14.1.0-1ubuntu1) ... 854s Setting up libaec0:arm64 (1.1.3-1) ... 854s Setting up python3-natsort (8.0.2-2) ... 854s Setting up unicode-data (15.1.0-1) ... 854s Setting up python3-decorator (5.1.1-5) ... 854s Setting up libblas3:arm64 (3.12.0-3build1) ... 854s 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 854s Setting up python3-packaging (24.0-1) ... 854s Setting up python3-wcwidth (0.2.5+dfsg1-1.1ubuntu1) ... 854s Setting up python3-typeshed (0.0~git20231111.6764465-3) ... 854s Setting up python3-executing (2.0.1-0.1) ... 854s Setting up python3-brotli (1.1.0-2build2) ... 854s Setting up liblzf1:arm64 (3.6-4) ... 854s Setting up python3-cycler (0.12.1-1) ... 855s Setting up libimagequant0:arm64 (2.18.0-1build1) ... 855s Setting up python3-kiwisolver (1.4.5-1) ... 855s Setting up libtcl8.6:arm64 (8.6.14+dfsg-1build1) ... 855s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 855s Setting up python3-pluggy (1.5.0-1) ... 855s Setting up python3-traitlets (5.5.0-2) ... 855s Setting up libxslt1.1:arm64 (1.1.39-0exp1build1) ... 855s Setting up libopenjp2-7:arm64 (2.5.0-2build3) ... 855s Setting up libharfbuzz0b:arm64 (8.3.0-2build2) ... 855s Setting up python3-dateutil (2.9.0-2) ... 855s Setting up libxss1:arm64 (1:1.2.3-1build3) ... 855s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... 855s Setting up python3-mpmath (1.3.0-1) ... 856s Setting up python-matplotlib-data (3.6.3-2ubuntu1) ... 856s Setting up libwebpmux3:arm64 (1.4.0-0.1) ... 856s Setting up python3-appdirs (1.4.4-4) ... 856s Setting up python3-stack-data (0.6.3-1) ... 856s Setting up libssw0:arm64 (1.1-14build1) ... 856s Setting up libsz2:arm64 (1.1.3-1) ... 856s Setting up python3-ptyprocess (0.7.0-5) ... 856s Setting up python3-prompt-toolkit (3.0.46-1) ... 857s Setting up python3-sympy (1.12-8) ... 863s Setting up liblapack3:arm64 (3.12.0-3build1) ... 863s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 863s Setting up libxft2:arm64 (2.3.6-1build1) ... 863s Setting up python3-jedi (0.19.1+ds1-1) ... 864s Setting up python3-pytest (8.2.2-1ubuntu1) ... 864s Setting up libtk8.6:arm64 (8.6.14-1build1) ... 864s Setting up python3-matplotlib-inline (0.1.6-2) ... 864s Setting up python3-fs (2.4.16-4) ... 865s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... 865s Setting up python3-pexpect (4.9-2) ... 865s Setting up libraqm0:arm64 (0.10.1-1build1) ... 865s Setting up python3-numpy (1:1.26.4+ds-10) ... 867s Setting up python3-hdmedians (0.14.2-5.1build1) ... 867s Setting up python3-lxml:arm64 (5.2.1-1) ... 867s Setting up python3-contourpy (1.0.7-3) ... 868s Setting up libhdf5-103-1t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 868s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 868s Setting up libhdf5-hl-100t64:arm64 (1.10.10+repack-3.1ubuntu4) ... 868s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ... 868s Setting up python3-scipy (1.11.4-10) ... 871s Setting up blt (2.5.3+dfsg-7build1) ... 871s Setting up python3-pandas-lib:arm64 (2.1.4+dfsg-8) ... 871s Setting up python3-h5py-serial (3.10.0-1ubuntu3) ... 871s Setting up python3-tk:arm64 (3.12.3-0ubuntu1) ... 871s Setting up python3-pil:arm64 (10.3.0-2) ... 872s Setting up python3-pandas (2.1.4+dfsg-8) ... 877s Setting up python3-pil.imagetk:arm64 (10.3.0-2) ... 877s Setting up python3-ipython (8.20.0-1ubuntu1) ... 878s Setting up python3-h5py (3.10.0-1ubuntu3) ... 878s Setting up python3-fonttools (4.46.0-1build2) ... 879s Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... 879s Setting up python3-matplotlib (3.6.3-2ubuntu1) ... 880s Setting up python3-skbio (0.5.9-4build1) ... 881s Setting up autopkgtest-satdep (0) ... 881s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 881s Processing triggers for man-db (2.12.1-1) ... 887s (Reading database ... 95297 files and directories currently installed.) 887s Removing autopkgtest-satdep (0) ... 888s autopkgtest [13:33:52]: test import-skbio: [----------------------- 891s autopkgtest [13:33:55]: test import-skbio: -----------------------] 892s import-skbio PASS 892s autopkgtest [13:33:56]: test import-skbio: - - - - - - - - - - results - - - - - - - - - - 892s autopkgtest [13:33:56]: test testsuite: preparing testbed 894s Reading package lists... 894s Building dependency tree... 894s Reading state information... 894s Starting pkgProblemResolver with broken count: 0 894s Starting 2 pkgProblemResolver with broken count: 0 894s Done 895s The following NEW packages will be installed: 895s autopkgtest-satdep 895s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 895s Need to get 0 B/716 B of archives. 895s After this operation, 0 B of additional disk space will be used. 895s Get:1 /tmp/autopkgtest.oIisQn/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 896s Selecting previously unselected package autopkgtest-satdep. 896s (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 ... 95297 files and directories currently installed.) 896s Preparing to unpack .../2-autopkgtest-satdep.deb ... 896s Unpacking autopkgtest-satdep (0) ... 896s Setting up autopkgtest-satdep (0) ... 900s (Reading database ... 95297 files and directories currently installed.) 900s Removing autopkgtest-satdep (0) ... 901s autopkgtest [13:34:05]: test testsuite: [----------------------- 901s + 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 {} ; 901s + 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 {} ; 901s + http_proxy=http://127.0.0.1:9 python3 -m pytest --pyargs skbio 906s ============================= test session starts ============================== 906s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 906s rootdir: /tmp/autopkgtest.oIisQn/autopkgtest_tmp 906s collected 2390 items 906s 906s skbio/alignment/tests/test_pairwise.py ......................... [ 1%] 906s skbio/alignment/tests/test_ssw.py ........................... [ 2%] 906s skbio/alignment/tests/test_tabular_msa.py .............................. [ 3%] 907s ........................................................................ [ 6%] 908s ........................................................................ [ 9%] 909s ........................................................................ [ 12%] 909s ........................................................................ [ 15%] 909s ........................................................................ [ 18%] 909s .......... [ 18%] 909s skbio/diversity/alpha/tests/test_ace.py .. [ 18%] 910s skbio/diversity/alpha/tests/test_base.py ........................ [ 20%] 910s skbio/diversity/alpha/tests/test_chao1.py ... [ 20%] 910s skbio/diversity/alpha/tests/test_faith_pd.py ........ [ 20%] 910s skbio/diversity/alpha/tests/test_gini.py .... [ 20%] 911s skbio/diversity/alpha/tests/test_lladser.py ............ [ 21%] 911s skbio/diversity/beta/tests/test_unifrac.py ............................ [ 22%] 911s skbio/diversity/tests/test_block.py ........... [ 22%] 911s skbio/diversity/tests/test_driver.py ................................... [ 24%] 911s [ 24%] 912s skbio/diversity/tests/test_util.py ........... [ 24%] 912s skbio/io/format/tests/test_base.py ................................ [ 26%] 912s skbio/io/format/tests/test_binary_dm.py ......... [ 26%] 912s skbio/io/format/tests/test_blast6.py ........... [ 26%] 913s skbio/io/format/tests/test_blast7.py .............. [ 27%] 913s skbio/io/format/tests/test_clustal.py ............. [ 27%] 915s skbio/io/format/tests/test_embl.py ............................... [ 29%] 915s skbio/io/format/tests/test_emptyfile.py .. [ 29%] 923s skbio/io/format/tests/test_fasta.py ................ [ 30%] 929s skbio/io/format/tests/test_fastq.py ............... [ 30%] 930s skbio/io/format/tests/test_genbank.py ..................... [ 31%] 930s skbio/io/format/tests/test_gff3.py ........................ [ 32%] 930s skbio/io/format/tests/test_lsmat.py ....... [ 32%] 931s skbio/io/format/tests/test_newick.py ....... [ 33%] 931s skbio/io/format/tests/test_ordination.py ..... [ 33%] 933s skbio/io/format/tests/test_phylip.py ....... [ 33%] 933s skbio/io/format/tests/test_qseq.py ...... [ 33%] 933s skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ 34%] 935s skbio/io/format/tests/test_stockholm.py ................................ [ 35%] 935s ........................................... [ 37%] 935s skbio/io/format/tests/test_taxdump.py ...... [ 37%] 935s skbio/io/tests/test_iosources.py .......... [ 37%] 935s skbio/io/tests/test_registry.py ........................................ [ 39%] 935s ...................................................... [ 41%] 937s skbio/io/tests/test_util.py .......................................XXsss [ 43%] 940s sssssssssssssssssssssssssss..................................xx......... [ 46%] 944s .........................xx..................................xx......... [ 49%] 945s .........................xx..... [ 51%] 948s skbio/metadata/tests/test_intersection.py ............... [ 51%] 948s skbio/metadata/tests/test_interval.py .................................. [ 53%] 948s ..................................... [ 54%] 948s skbio/metadata/tests/test_mixin.py ..................................... [ 56%] 948s ............................................................. [ 58%] 948s skbio/sequence/tests/test_distance.py .......................... [ 59%] 948s skbio/sequence/tests/test_dna.py .... [ 59%] 948s skbio/sequence/tests/test_genetic_code.py .......................... [ 61%] 948s skbio/sequence/tests/test_grammared_sequence.py ........................ [ 62%] 948s ................... [ 62%] 948s skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ 63%] 948s ....... [ 64%] 948s skbio/sequence/tests/test_protein.py .......... [ 64%] 948s skbio/sequence/tests/test_rna.py .... [ 64%] 948s skbio/sequence/tests/test_sequence.py .................................. [ 66%] 948s ........................................................................ [ 69%] 948s ........................................................................ [ 72%] 948s ........................................................................ [ 75%] 948s ....... [ 75%] 949s skbio/stats/distance/tests/test_anosim.py .... [ 75%] 949s skbio/stats/distance/tests/test_base.py ................................ [ 76%] 950s ................................................................... [ 79%] 956s skbio/stats/distance/tests/test_bioenv.py ................. [ 80%] 958s skbio/stats/distance/tests/test_mantel.py .............................. [ 81%] 958s .............. [ 82%] 958s skbio/stats/distance/tests/test_permanova.py .... [ 82%] 963s skbio/stats/distance/tests/test_permdisp.py ............. [ 82%] 963s skbio/stats/evolve/tests/test_hommola.py ............ [ 83%] 963s skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ 83%] 963s ..... [ 83%] 963s skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ 84%] 964s skbio/stats/ordination/tests/test_ordination_results.py ................ [ 84%] 964s [ 84%] 964s skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ 84%] 964s ....... [ 85%] 965s skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ 85%] 965s skbio/stats/ordination/tests/test_util.py .......... [ 85%] 965s skbio/stats/tests/test_composition.py .................................. [ 87%] 965s ............................... [ 88%] 965s skbio/stats/tests/test_gradient.py .......................... [ 89%] 965s skbio/stats/tests/test_misc.py ... [ 89%] 967s skbio/stats/tests/test_power.py ........................................ [ 91%] 968s ... [ 91%] 968s skbio/stats/tests/test_subsample.py ............ [ 92%] 968s skbio/tests/test_base.py ..... [ 92%] 968s skbio/tests/test_workflow.py ................. [ 92%] 968s skbio/tree/tests/test_majority_rule.py ...... [ 93%] 968s skbio/tree/tests/test_nj.py ........... [ 93%] 968s skbio/tree/tests/test_tree.py .......................................... [ 95%] 968s ................................................... [ 97%] 968s skbio/util/tests/test_decorator.py ....................... [ 98%] 968s skbio/util/tests/test_misc.py .................... [ 99%] 968s skbio/util/tests/test_testing.py ............... [100%] 968s 968s =============================== warnings summary =============================== 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_kwargs_are_usable 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_DNA 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_same_as_using_StripedSmithWaterman_object_Protein 968s skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_type_mismatch 968s /tmp/autopkgtest.oIisQn/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 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 968s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_constructor_makes_shallow_copy_of_positional_metadata 968s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_constructor_makes_shallow_copy_of_positional_metadata 968s /tmp/autopkgtest.oIisQn/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]` 968s df['bar'][0].append(42) 968s 968s skbio/alignment/tests/test_tabular_msa.py::TestTabularMSAPositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 968s skbio/metadata/tests/test_mixin.py::TestPositionalMetadataMixin::test_positional_metadata_setter_makes_shallow_copy 968s skbio/sequence/tests/test_sequence.py::TestSequencePositionalMetadata::test_positional_metadata_setter_makes_shallow_copy 968s /tmp/autopkgtest.oIisQn/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]` 968s df['bar'][0].append(42) 968s 968s skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/alignment/_tabular_msa.py:1653: RuntimeWarning: invalid value encountered in divide 968s gap_freqs /= length 968s 968s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: invalid value encountered in scalar divide 968s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 968s 968s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/diversity/alpha/_base.py:887: RuntimeWarning: invalid value encountered in divide 968s freqs = counts / counts.sum() 968s 968s skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/diversity/alpha/_base.py:811: RuntimeWarning: divide by zero encountered in log 968s return shannon(counts, base=np.e) / np.log(observed_otus(counts)) 968s 968s skbio/diversity/tests/test_block.py: 3 warnings 968s skbio/diversity/tests/test_driver.py: 9 warnings 968s /tmp/autopkgtest.oIisQn/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. 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates 968s /tmp/autopkgtest.oIisQn/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 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars 968s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 968s skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars 968s /tmp/autopkgtest.oIisQn/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 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates 968s /tmp/autopkgtest.oIisQn/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 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/sequence/_sequence.py:1820: RuntimeWarning: invalid value encountered in divide 968s obs_counts = obs_counts / len(self) 968s 968s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/distance/_mantel.py:354: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 968s warnings.warn(ConstantInputWarning()) 968s 968s skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/distance/_mantel.py:473: ConstantInputWarning: All values in data are exactly equal; results may not be reliable. 968s warnings.warn(ConstantInputWarning()) 968s 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations 968s /tmp/autopkgtest.oIisQn/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. 968s warn( 968s 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups 968s /tmp/autopkgtest.oIisQn/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. 968s warn( 968s 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/ordination/_principal_coordinate_analysis.py:188: RuntimeWarning: invalid value encountered in divide 968s proportion_explained = eigvals / sum_eigenvalues 968s 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null 968s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal 968s /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 968s warnings.warn(stats.ConstantInputWarning(msg)) 968s 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 968s skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results 968s /tmp/autopkgtest.oIisQn/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. 968s warn( 968s 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg 968s /tmp/autopkgtest.oIisQn/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. 968s fig.tight_layout() 968s 968s skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/ordination/_ordination_results.py:263: UserWarning: No data for colormapping provided via 'c'. Parameters 'cmap' will be ignored 968s plot = scatter_fn(c=point_colors, cmap=cmap) 968s 968s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape 968s /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is deprecated to return a value that is not None from a test case (>) 968s return self.run(*args, **kwds) 968s 968s skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAResults_biplot_score::test_biplot_score 968s /tmp/autopkgtest.oIisQn/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]` 968s scaling = (rda_.eigvals[0] / rda_.eigvals[:6]) 968s 968s skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test 968s /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. 968s res = hypotest_fun_out(*samples, **kwds) 968s 968s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/composition.py:982: RuntimeWarning: divide by zero encountered in log 968s X_log = np.log(mat) 968s 968s skbio/stats/tests/test_composition.py::TestVLR::test_pairwise_vlr 968s /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: RuntimeWarning: invalid value encountered in subtract 968s X -= avg[:, None] 968s 968s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 968s /tmp/autopkgtest.oIisQn/autopkgtest_tmp/skbio/stats/composition.py:837: RuntimeWarning: divide by zero encountered in log 968s x = np.log(x) 968s 968s skbio/stats/tests/test_composition.py::TestVLR::test_vlr 968s /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: invalid value encountered in subtract 968s x = asanyarray(arr - arrmean) 968s 968s skbio/stats/tests/test_gradient.py: 13 warnings 968s /tmp/autopkgtest.oIisQn/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]` 968s np.abs((w_vector[i] - w_vector[i-1])) 968s 968s skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector 968s /tmp/autopkgtest.oIisQn/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. 968s trajectories.loc[idx] = ( 968s 968s skbio/stats/tests/test_power.py: 27 warnings 968s /tmp/autopkgtest.oIisQn/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.) 968s pwr[id2] = _calculate_power(ps, a) 968s 968s skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output 968s /tmp/autopkgtest.oIisQn/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(). 968s warnings.warn('%s is deprecated as of scikit-bio version %s, and ' 968s 968s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 968s = 2350 passed, 30 skipped, 8 xfailed, 2 xpassed, 119 warnings in 66.93s (0:01:06) = 970s autopkgtest [13:35:14]: test testsuite: -----------------------] 970s testsuite PASS 970s autopkgtest [13:35:14]: test testsuite: - - - - - - - - - - results - - - - - - - - - - 971s autopkgtest [13:35:15]: @@@@@@@@@@@@@@@@@@@@ summary 971s import-skbio PASS 971s testsuite PASS 1044s nova [W] Skipping flock in bos03-arm64 1044s Creating nova instance adt-oracular-arm64-python-skbio-20240608-131904-juju-7f2275-prod-proposed-migration-environment-2-71d73ab4-78ee-4564-b8a5-d9036624d3da from image adt/ubuntu-oracular-arm64-server-20240608.img (UUID 22fa5d69-8269-442f-bb5d-fd1454f7b08f)...